ambertools: Version bump to 12

5 files changed, 16265 insertions, 0 deletions

diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog
index 6e9d91d38..59197eb4b 100644
--- a/sci-chemistry/ambertools/ChangeLog
+++ b/sci-chemistry/ambertools/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ChangeLog,v 1.2 2011/08/02 14:42:37 alexxy Exp $
 
+*ambertools-12 (20 Oct 2012)
+
+  20 Oct 2012; Reinis Danne <rei4dan@gmail.com> +ambertools-12.ebuild,
+  +files/ambertools-12-bugfix_14-26.patch, +files/ambertools-12-gentoo.patch:
+  Bump to 12.
+
 *ambertools-1.5-r4 (28 Aug 2012)
 
   28 Aug 2012; Reinis Danne <rei4dan@gmail.com> +ambertools-1.5-r4.ebuild,
diff --git a/sci-chemistry/ambertools/Manifest b/sci-chemistry/ambertools/Manifest
index 55f45b80a..5ccd71741 100644
--- a/sci-chemistry/ambertools/Manifest
+++ b/sci-chemistry/ambertools/Manifest
@@ -1 +1,2 @@
 DIST AmberTools-1.5.tar.bz2 121062582 SHA256 0c7d397d2e91603bb9123ae68e91af3525269e60800ced360f68c13350651d7c SHA512 3366bfe6d0ee1f9b5b99b1d6aad4111093919fe43ab5e9753c62ae815dca958bfc660a3af9db83de71690624869ee5e47af51a6c8412c6bdcb32aecbefb01677 WHIRLPOOL 192f027f5480807cd36693c6c7d8e3b809f4032ecb1a1bf97df888bd02974fbd2bc8da4ea0e9d52062dce10e969bb72cc2f1ba9c4d627f6097492175ab025120
+DIST AmberTools12.tar.bz2 89175545 SHA256 aff5dbc29b5b5b29a85ae465d3e250e225cd85deb2bce828833c2dc769e81009 SHA512 4c34d460fdedf00ade847040856d4bf7df65e7370d4a696dd858fdd3612c192ddc13dabde559bc1a7ae4068ba8040ee159479e247b2c1e59ed976a5aa6344970 WHIRLPOOL 3bc134875482d00d0d1861e9d87f4fef9fdebd1f6860b2c4623f48c23f6f8673df4b23069f3e9374ef9814d500f23f986250a1bcae093597c9e0a0c9d40d6c86
diff --git a/sci-chemistry/ambertools/ambertools-12.ebuild b/sci-chemistry/ambertools/ambertools-12.ebuild
new file mode 100644
index 000000000..31d6f8e89
--- /dev/null
+++ b/sci-chemistry/ambertools/ambertools-12.ebuild
@@ -0,0 +1,151 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils fortran-2 toolchain-funcs
+
+DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
+HOMEPAGE="http://ambermd.org/#AmberTools"
+SRC_URI="
+	AmberTools${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+IUSE="openmp X"
+
+RESTRICT="fetch"
+
+RDEPEND="
+	virtual/cblas
+	virtual/lapack
+	sci-libs/clapack
+	sci-libs/arpack
+	sci-libs/cifparse-obj
+	sci-chemistry/mopac7
+	sci-libs/netcdf
+	sci-libs/fftw:3.0
+	sci-chemistry/reduce"
+DEPEND="${RDEPEND}
+	app-shells/tcsh
+	dev-util/byacc
+	dev-libs/libf2c
+	sys-devel/ucpp"
+
+S="${WORKDIR}/amber12"
+
+pkg_nofetch() {
+	einfo "Go to ${HOMEPAGE} and get ${A}"
+	einfo "Place it in ${DISTDIR}"
+}
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	if use openmp; then
+		tc-has-openmp || \
+			die "Please select an openmp capable compiler like gcc[openmp]"
+	fi
+	AMBERHOME="${S}"
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}/${P}-bugfix_14-26.patch" \
+		"${FILESDIR}/${P}-gentoo.patch"
+	cd "${S}"/AmberTools/src
+	rm -r \
+		arpack \
+		blas \
+		byacc \
+		lapack \
+		fftw-3.3 \
+		c9x-complex \
+		cifparse \
+		netcdf \
+		reduce \
+		ucpp-1.3 \
+		|| die
+}
+
+src_configure() {
+	cd "${S}"/AmberTools/src
+	sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
+		-e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \
+		-e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \
+		-e "s:GENTOO_CFLAGS:${CFLAGS} -DBINTRAJ :g" \
+		-e "s:GENTOO_CXXFLAGS:${CXXFLAGS}:g" \
+		-e "s:GENTOO_FFLAGS:${FFLAGS}:g" \
+		-e "s:GENTOO_LDFLAGS:${LDFLAGS}:g" \
+		-e "s:GENTOO_INCLUDE:${EPREFIX}/usr/include:g" \
+		-e "s:GENTOO_FFTW3_LIBS:$(pkg-config fftw3 --libs):" \
+		-e "s:fc=g77:fc=$(tc-getFC):g" \
+		-e "s:\$netcdfflag:$(pkg-config netcdf --libs):g" \
+		-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
+		-i configure2 || die
+	sed -e "s:arsecond_:arscnd_:g" \
+		-i sff/time.c \
+		-i sff/sff.h \
+		-i sff/sff.c || die
+
+	local myconf="--no-updates"
+
+	use X || myconf="${myconf} -noX11"
+
+	use openmp && myconf="${myconf} -openmp"
+
+	cd "${S}"
+	./configure \
+		${myconf} \
+		-nobintraj \
+		-nomtkpp \
+		gnu
+}
+
+src_compile() {
+	cd "${S}"/AmberTools/src
+	emake
+}
+
+src_test() {
+	cd "${S}"/AmberTools/test
+	emake test
+}
+
+src_install() {
+	rm bin/*.py
+
+	for x in bin/*
+	do
+		[ ! -d ${x} ] && dobin ${x}
+	done
+
+	dobin AmberTools/src/antechamber/mopac.sh
+	sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \
+		-i "${ED}/usr/bin/mopac.sh" || die
+
+	# Make symlinks untill binpath for amber will be fixed
+	dodir /usr/share/${PN}/bin
+	cd "${ED}/usr/bin"
+	for x in *
+		do dosym /usr/bin/${x} /usr/share/${PN}/bin/${x}
+	done
+	cd "${S}"
+
+	dodoc doc/AmberTools12.pdf
+	dolib.a lib/*
+	insinto /usr/include/${PN}
+	doins include/*
+	insinto /usr/share/${PN}
+	doins -r dat
+	cd AmberTools
+	doins -r benchmarks
+	doins -r examples
+	doins -r test
+
+	cat >> "${T}"/99ambertools <<- EOF
+	AMBERHOME="${EPREFIX}/usr/share/ambertools"
+	EOF
+	doenvd "${T}"/99ambertools
+}
diff --git a/sci-chemistry/ambertools/files/ambertools-12-bugfix_14-26.patch b/sci-chemistry/ambertools/files/ambertools-12-bugfix_14-26.patch
new file mode 100644
index 000000000..da9712cbb
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-12-bugfix_14-26.patch
@@ -0,0 +1,14856 @@
+diff --git a/AmberTools/src/configure2 b/AmberTools/src/configure2
+index 25d3f0a..9ce5ef0 100755
+--- a/AmberTools/src/configure2
++++ b/AmberTools/src/configure2
+@@ -24,17 +24,19 @@ Usage: ./configure [flags] compiler
+                      in your PATH; Note: you must first configure and build 
+                      a serial AmberTools.
+       -cuda          Builds the NVIDIA GPU version of pmemd (pmemd.cuda and
+-                     pmemd.cuda.MPI) with default SPDP hybrid precision.
++                     pmemd.cuda.MPI) with default SPFP mixed single/double/
++                     fixed-point precision.
+                      (Note: Set CUDA_HOME to your cuda build tools installation
+                      path.)
+-      -cuda_SPDP     Currently just an alias to CUDA
+-      -cuda_DPDP     Builds the NVIDIA GPU version of pmemd (pmemd.cuda and
+-                     pmemd.cuda.MPI) with full double precision. (Considerably
+-                     slower than SPDP for many cards without a meaningful gain
+-                     in accuracy)
+-      -cuda_SPSP     Builds the NVIDIA GPU version of pmemd (pmemd.cuda and
+-                     pmemd.cuda.MPI) with full single precision. (Not a good
+-                     choice for production runs!)
++      -cuda_SPDP     Builds the NVIDIA GPU version of pmemd (pmemd_SPDP.cuda and
++                     pmemd.cuda_SPDP.MPI) with SPDP hybrid precision. (This was
++                     the default for previous versions of AMBER but has now been
++                     superseded by the SPFP mixed precision model).
++      -cuda_DPDP     Builds the NVIDIA GPU version of pmemd (pmemd.cuda_DPDP and
++                     pmemd.cuda_DPDP.MPI) with full double precision. (Considerably
++                     slower than SPDP and SPFP for many cards without a meaningful
++                     gain in accuracy)
++      -cuda_SPFP     Currently an alias to -cuda.
+       -openmp        Use OpenMP pragmas to parallelize NAB and paramfit
+                      (not available for pgi).
+                      Do not use -openmp and -mpi at the same time. Type "make
+@@ -149,8 +151,8 @@ fi
+ #------------------------------------------------------------------------------
+ mpi='no'
+ mpinab=''
+-cuda='no'
+-cuda_SPSP='no'
++cuda_SPFP='no'
++cuda_SPDP='no'
+ cuda_DPDP='no'
+ scali='no'
+ scalapack='no'
+@@ -222,9 +224,9 @@ if [ $# -lt 1 ]; then usage; fi
+ while [ $# -gt 0 ]; do
+     case "$1" in
+         -mpi)           mpi='yes'; mpinab='mpi'; mdgx='no';mtkpp='' ;;
+-        -cuda)          cuda='yes';rism='no';pbsaflag='';mdgx='no';mtkpp='' ;;
+-        -cuda_SPDP)     cuda='yes';rism='no';pbsaflag='';mdgx='no';mtkpp='' ;;
+-        -cuda_SPSP)     cuda_SPSP='yes';rism='no';pbsaflag='';mdgx='no';mtkpp='' ;;
++        -cuda)          cuda_SPFP='yes';rism='no';pbsaflag='';mdgx='no';mtkpp='' ;;
++        -cuda_SPFP)     cuda_SPFP='yes';rism='no';pbsaflag='';mdgx='no';mtkpp='' ;;
++        -cuda_SPDP)     cuda_SPDP='yes';rism='no';pbsaflag='';mdgx='no';mtkpp='' ;;
+         -cuda_DPDP)     cuda_DPDP='yes';rism='no';pbsaflag='';mdgx='no';mtkpp='' ;;
+         -scali)         scali='yes' ;;
+         -scalapack)     scalapack='yes' ;;
+@@ -443,22 +445,22 @@ if [ "$noX11" = "false" ]; then
+         echo "       On old Fedora OS's install the xorg-x11-devel package."
+         echo "       On RedHat OS's install the XFree86-devel package."
+         echo "       On Ubuntu OS's install the xorg-dev package."
+-	echo "       To build Amber without XLEaP, re-run configure with '-no-X11:"
+-        echo "            `mod_command_args '' '-no-X11'`"
+-	exit 1
++        echo "       To build Amber without XLEaP, re-run configure with '-noX11:"
++        echo "            `mod_command_args '' '-noX11'`"
++        exit 1
+     fi
+ 
+     if [ -d /usr/include/X11/extensions ]
+     then
+         empty_statement=
+-    else
++    elif [ "$is_mac" = "no" ]; then
+         echo "ERROR: the X11 extensions headers are not in the usual location!"
+         echo "       To search for them try the command: locate X11/extensions"
+         echo "       On new Fedora OSes install libXext-devel"
+         echo "       On RedHat OSes install libXext-devel"
+-	echo "       To build Amber without XLEaP, re-run configure with '-no-X11:"
+-        echo "            `mod_command_args '' '-no-X11'`"
+-	exit 1
++        echo "       To build Amber without XLEaP, re-run configure with '-noX11:"
++        echo "            `mod_command_args '' '-noX11'`"
++        exit 1
+     fi
+ fi
+ 
+@@ -544,7 +546,7 @@ fi
+ #------------------------------------------------------------------------------
+ #  Determine which type of installation we're doing
+ #------------------------------------------------------------------------------
+-if [ "$cuda" = 'yes' -o "$cuda_SPSP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
++if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPDP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
+    if [ "$mpi" = 'yes' ]; then
+       installtype='cuda_parallel'
+    else
+@@ -559,7 +561,7 @@ fi
+ #------------------------------------------------------------------------------
+ #  Check for cuda incompatibilities or missing files:
+ #------------------------------------------------------------------------------
+-if [ "$cuda" = 'yes' -o "$cuda_SPSP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
++if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPDP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
+     if [ -z "$CUDA_HOME" ]; then
+         echo "Error: CUDA_HOME is not set. This must point to your NVIDIA tools installation"
+         exit 1
+@@ -572,25 +574,26 @@ if [ "$cuda" = 'yes' -o "$cuda_SPSP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
+         echo "Error: nvcc cuda compiler not found in $CUDA_HOME/bin/"
+         exit 1
+     fi
+-    #Check for mixing of cuda with cuda_SPSP or cuda_DPDP debugging options.
+-    #cuda      = SPDP mixed precision (default)
+-    #cuda_SPSP = SPSP single precision only - except shake (debug option!)
++    #Check for mixing of cuda with cuda_SPDP or cuda_DPDP debugging options.
++    #cuda      = SPFP mixed single/double/fixed-point precision (default)
++    #cuda_SPFP = SPFP mixed single/double/fixed-point precision (default)
++    #cuda_SPDP = SPDP hybrid single/double precision (debug option!)
+     #cuda_DPDP = DPDP double precision only (debug option!)
+-    if [ "$cuda" = 'yes' ]; then
+-      if [ "$cuda_SPSP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
+-        echo "Error: specification of -cuda, -cuda_SPSP and -cuda_DPDP are mutually exclusive"
++    if [ "$cuda_SPFP" = 'yes' ]; then
++      if [ "$cuda_SPDP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
++        echo "Error: specification of -cuda, -cuda_SPDP and -cuda_DPDP are mutually exclusive"
+         exit 1
+       fi
+     fi
+-    if [ "$cuda_SPSP" = 'yes' ]; then
+-      if [ "$cuda" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
+-        echo "Error: specification of -cuda, -cuda_SPSP and -cuda_DPDP are mutually exclusive"
++    if [ "$cuda_SPDP" = 'yes' ]; then
++      if [ "$cuda_SPFP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
++        echo "Error: specification of -cuda, -cuda_SPDP and -cuda_DPDP are mutually exclusive"
+         exit 1
+       fi
+     fi
+     if [ "$cuda_DPDP" = 'yes' ]; then
+-      if [ "$cuda" = 'yes' -o "$cuda_SPSP" = 'yes' ]; then
+-        echo "Error: specification of -cuda, -cuda_SPSP and -cuda_DPDP are mutually exclusive"
++      if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPDP" = 'yes' ]; then
++        echo "Error: specification of -cuda, -cuda_SPDP and -cuda_DPDP are mutually exclusive"
+         exit 1
+       fi
+     fi
+@@ -736,14 +739,15 @@ gnu)
+     pmemd_coptflags="$coptflags"
+ 
+     #CUDA Specifics
+-    if [ "$cuda" = 'yes' -o "$cuda_SPSP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
++    if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPDP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
+       pmemd_cu_includes='-I$(CUDA_HOME)/include -IB40C -IB40C/KernelCommon'
+       pmemd_cu_defines='-DCUDA'
+       pmemd_cu_libs='./cuda/cuda.a -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib -lcurand -lcufft -lcudart'
+       if [ "$optimise" = 'no' ]; then
+-        nvcc='$(CUDA_HOME)/bin/nvcc -use_fast_math -O0 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20'
++        nvcc='$(CUDA_HOME)/bin/nvcc -use_fast_math -O0 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30'
+       else
+-        nvcc='$(CUDA_HOME)/bin/nvcc -use_fast_math -O3 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20'
++	#2012/05/30 - Removed -O3 here because of 'possible' performance regression. - Scott sees this. Ross can't reproduce it.
++        nvcc='$(CUDA_HOME)/bin/nvcc -use_fast_math -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30'
+       fi
+       if [ "$mpi" = 'yes' ]; then
+         mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'`
+@@ -752,8 +756,11 @@ gnu)
+         pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK"
+       fi
+     fi
+-    if [ "$cuda_SPSP" = 'yes' ]; then
+-      pmemd_cu_defines="$pmemd_cu_defines -Duse_SPSP"
++    if [ "$cuda_SPFP" = 'yes' ]; then
++      pmemd_cu_defines="$pmemd_cu_defines -Duse_SPFP"
++    fi
++    if [ "$cuda_SPDP" = 'yes' ]; then
++      pmemd_cu_defines="$pmemd_cu_defines -Duse_SPDP"
+     fi
+     if [ "$cuda_DPDP" = 'yes' ]; then
+       pmemd_cu_defines="$pmemd_cu_defines -Duse_DPDP"
+@@ -1001,7 +1008,7 @@ intel)
+       fi
+ 
+       #CUDA Specifics
+-      if [ "$cuda" = 'yes' -o "$cuda_SPSP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
++      if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPDP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
+ 
+         # -ipo (multi-file Interprocedural Optimizations optimizations) causes issues with 
+         #  CUDA c code linking. Leave at a single-file IPO for the moment MJW
+@@ -1012,9 +1019,10 @@ intel)
+         pmemd_cu_defines='-DCUDA'
+         pmemd_cu_libs='./cuda/cuda.a -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib -lcurand -lcufft -lcudart'
+         if [ "$optimise" = 'yes' ]; then
+-            nvcc='$(CUDA_HOME)/bin/nvcc -use_fast_math -O3 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20'
++	#2012/05/30 - Removed -O3 here because of 'possible' performance regression. - Scott sees this. Ross can't reproduce it.
++            nvcc='$(CUDA_HOME)/bin/nvcc -use_fast_math -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30'
+         else
+-            nvcc='$(CUDA_HOME)/bin/nvcc -use_fast_math -O0 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20'
++            nvcc='$(CUDA_HOME)/bin/nvcc -use_fast_math -O0 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30'
+         fi
+ 
+         if [ "$mpi" = 'yes' ]; then
+@@ -1024,8 +1032,11 @@ intel)
+           pmemd_coptflags="$pmemd_coptflags -DMPICH_IGNORE_CXX_SEEK"
+         fi
+       fi
+-      if [ "$cuda_SPSP" = 'yes' ]; then
+-        pmemd_cu_defines="$pmemd_cu_defines -Duse_SPSP"
++      if [ "$cuda_SPFP" = 'yes' ]; then
++        pmemd_cu_defines="$pmemd_cu_defines -Duse_SPFP"
++      fi
++      if [ "$cuda_SPDP" = 'yes' ]; then
++        pmemd_cu_defines="$pmemd_cu_defines -Duse_SPDP"
+       fi
+       if [ "$cuda_DPDP" = 'yes' ]; then
+         pmemd_cu_defines="$pmemd_cu_defines -Duse_DPDP"
+@@ -1131,7 +1142,7 @@ pgi)
+         foptflags="$foptflags -fastsse"
+     fi
+ 
+-    if [ "$cuda" = "yes" -o "$cuda_SPSP" = "yes" -o "$cuda_DPDP" = "yes" ]; then
++    if [ "$cuda_SPFP" = "yes" -o "$cuda_SPDP" = "yes" -o "$cuda_DPDP" = "yes" ]; then
+         echo "ERROR: cuda is not available for pgi."
+         echo "       Please re-run configure without CUDA flags to use this compiler:"
+         echo "            `mod_command_args '-cuda -cuda_SPDP -cuda_DPDP' ''`"
+@@ -1258,7 +1269,7 @@ solaris)
+         flibs_arch="$flibs_arch $SCALAPACKHOME/scalapack_SUN64.a $BLACSHOME/blacsF77init_MPI-SUN64-0.a $BLACSHOME/blacs_MPI-SUN64-0.a $BLACSHOME/blacsCinit_MPI-SUN64-0.a -lmpi"
+     fi
+ 
+-    if [ "$cuda" = 'yes' -o "$cuda_SPSP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
++    if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPDP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
+         echo "ERROR: cuda is not available for solaris."
+         echo "       Please re-run configure without CUDA flags to use this compiler:"
+         echo "            `mod_command_args '-cuda -cuda_SPDP -cuda_DPDP' ''`"
+@@ -1306,6 +1317,13 @@ open64)
+        echo "open64 setting is experimental."
+     fi
+ 
++    if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPDP" = 'yes' -o "$cuda_DPDP" = 'yes' ]; then
++        echo "ERROR: CUDA is not compatible with this compiler"
++        echo "       Please re-run configure without CUDA flags to use this compiler:"
++        echo "            `mod_command_args '-cuda -cuda_SPDP -cuda_DPDP' ''`"
++        exit 1
++    fi
++
+     if [ "$mpi" = 'yes' ]; then
+        ld=' mpif90 '
+     else
+diff --git a/AmberTools/src/cpptraj/src/ActionList.cpp b/AmberTools/src/cpptraj/src/ActionList.cpp
+index db3a157..f999e7f 100644
+--- a/AmberTools/src/cpptraj/src/ActionList.cpp
++++ b/AmberTools/src/cpptraj/src/ActionList.cpp
+@@ -33,6 +33,7 @@
+ #include "Action_Rotdif.h"
+ #include "Action_RunningAvg.h"
+ #include "Action_RmsAvgCorr.h"
++#include "Action_AutoImage.h"
+ 
+ // CONSTRUCTOR
+ ActionList::ActionList() {
+@@ -77,7 +78,7 @@ int ActionList::AddAction(ArgList &argIn) {
+   else if (argIn.CommandIs("secstruct"))      {Act=new DSSP;    }
+   else if (argIn.CommandIs("center"))         {Act=new Center;  }
+   else if (argIn.CommandIs("hbond"))          {Act=new Hbond;   }
+-  else if (argIn.CommandIs("image"))          {Act=new Image;   }
++  else if (argIn.CommandIs("image"))          {Act=new Action_Image;   }
+   else if (argIn.CommandIs("surf"))           {Act=new Surf;    }
+   else if (argIn.CommandIs("radgyr"))         {Act=new Radgyr;  }
+   else if (argIn.CommandIs("mask"))           {Act=new ActionMask;}
+@@ -101,6 +102,7 @@ int ActionList::AddAction(ArgList &argIn) {
+   else if (argIn.CommandIs("runningaverage")) {Act=new RunningAvg;}
+   else if (argIn.CommandIs("runavg"))         {Act=new RunningAvg;}
+   else if (argIn.CommandIs("rmsavgcorr"))     {Act=new RmsAvgCorr;}
++  else if (argIn.CommandIs("autoimage"))      {Act=new Action_AutoImage;}
+   // PTRAJ
+   else if (argIn.CommandIs("atomicfluct") ||
+            argIn.CommandIs("atomicfluct3D") ||
+diff --git a/AmberTools/src/cpptraj/src/Action_AutoImage.cpp b/AmberTools/src/cpptraj/src/Action_AutoImage.cpp
+index e69de29..ca61dc6 100644
+--- a/AmberTools/src/cpptraj/src/Action_AutoImage.cpp
++++ b/AmberTools/src/cpptraj/src/Action_AutoImage.cpp
+@@ -0,0 +1,273 @@
++#include "Action_AutoImage.h"
++#include "CpptrajStdio.h"
++#include "DistRoutines.h"
++
++// CONSTRUCTOR
++Action_AutoImage::Action_AutoImage() :
++  origin_(false),
++  ortho_(false),
++  center_(false),
++  truncoct_(false),
++  triclinic_(OFF)
++{}
++
++// Action_AutoImage::init()
++/** Usage: autoimage <mask> | anchor <mask> [fixed <fmask>] [mobile <mmask>]
++  *                  [origin] [familiar | triclinic]
++  */
++int Action_AutoImage::init() {
++  // Get keywords
++  origin_ = actionArgs.hasKey("origin");
++  center_ = actionArgs.hasKey("center");
++  if (actionArgs.hasKey("familiar")) triclinic_ = FAMILIAR;
++  if (actionArgs.hasKey("triclinic")) triclinic_ = FORCE;
++  anchor_ = actionArgs.getKeyString("anchor",NULL);
++  fixed_  = actionArgs.getKeyString("fixed",NULL);
++  mobile_ = actionArgs.getKeyString("mobile",NULL);
++  // Get mask expression for anchor if none yet specified
++  if (anchor_==NULL)  
++    anchor_ = actionArgs.getNextMask();
++
++  mprintf("    AUTOIMAGE: To");
++  if (origin_)
++    mprintf(" origin");
++  else
++    mprintf(" box center");
++  mprintf(" based on");
++  if (center_)
++    mprintf(" center of mass");
++  else
++    mprintf(" first atom position");
++  if (anchor_!=NULL)
++    mprintf(", anchor mask is [%s]\n", anchor_);
++  else
++    mprintf(", anchor is first molecule.\n");
++  if (fixed_!=NULL)
++    mprintf("\tAtoms in mask [%s] will be fixed to anchor region.\n", fixed_);
++  if (mobile_!=NULL)
++    mprintf("\tAtoms in mask [%s] will be imaged independently of anchor region.\n",
++            mobile_);
++
++  return 0;
++}
++
++// Action_AutoImage::SetupAtomRanges()
++/** Based on the given atom mask expression determine what molecules are
++  * selected by the mask.
++  * \return A list of atom pairs that mark the beginning and end of each
++  *         selected molecule.
++  */
++Action_AutoImage::pairList Action_AutoImage::SetupAtomRanges( const char* maskexpr )
++{
++  pairList imageList;
++  AtomMask Mask1;
++  if (Mask1.SetMaskString( (char*)maskexpr )) return imageList;
++
++  if (currentParm->SetupCharMask( Mask1, activeReference )) return imageList;
++  if (Mask1.None()) return imageList;
++
++  int* AtomsPerMol = currentParm->AtomsPerMol_ptr();
++  int firstAtom = 0;
++  int lastAtom = 0;
++  for (int molnum = 0; molnum < currentParm->Nmol(); ++molnum)
++  {
++    firstAtom = lastAtom;
++    lastAtom += AtomsPerMol[ molnum ];
++    // Check that each atom in the range is in Mask1
++    bool rangeIsValid = true;
++    for (int atom = firstAtom; atom < lastAtom; ++atom) {
++      if (!Mask1.AtomInCharMask(atom)) {
++        rangeIsValid = false;
++        break;
++      }
++    }
++    if (rangeIsValid) {
++      imageList.push_back( firstAtom );
++      imageList.push_back( lastAtom );
++    }
++  }
++  mprintf("\tMask [%s] corresponds to %zu molecules\n", Mask1.MaskString(), imageList.size()/2);
++  return imageList;
++}
++
++// Action_AutoImage::setup()
++int Action_AutoImage::setup() {
++  bool fixedauto = false;
++  bool mobileauto = false;
++
++  // Require molecule info
++  int* AtomsPerMol = currentParm->AtomsPerMol_ptr();
++  if (AtomsPerMol == NULL) {
++    mprinterr("Error: AutoImage: No molecule information in %s\n", currentParm->parmName);
++    return 1;
++  }
++  // Determine Box info
++  if (currentParm->boxType==NOBOX) {
++    mprintf("Warning: Image::setup: Parm %s does not contain box information.\n",
++            currentParm->parmName);
++    return 1;
++  }
++  ortho_ = false;
++  if (currentParm->boxType==ORTHO && triclinic_==OFF) ortho_=true;
++  // If box is originally truncated oct and not forcing triclinic, 
++  // turn familiar on.
++  if (AmberIfbox( currentParm->Box[4] )==2 && triclinic_!=FORCE && triclinic_!=FAMILIAR) {
++    mprintf("\tOriginal box is truncated octahedron, turning on 'familiar'.\n");
++    triclinic_=FAMILIAR;
++  }
++
++  // Set up anchor region
++  if (anchor_!=NULL) {
++    anchorList_ = SetupAtomRanges( anchor_ );
++  } else {
++    anchorList_.clear();
++    anchorList_.push_back( 0 );
++    anchorList_.push_back( AtomsPerMol[0] );
++  }
++  if (anchorList_.empty() || anchorList_.size() > 2) {
++    mprinterr("Error: Anchor mask [%s] corresponds to %zu mols, should only be 1.\n",
++              anchor_, anchorList_.size() / 2);
++    return 1;
++  }
++  // Set up mask for centering anchor
++  anchorMask_.AddAtomRange( anchorList_[0], anchorList_[1] );
++  int anchormolnum = currentParm->atomToMolecule( anchorList_[0] );
++  mprintf("\tAnchor molecule is %i\n", anchormolnum+1);
++  // Set up fixed region
++  if (fixed_!=NULL) 
++    fixedList_ = SetupAtomRanges( fixed_ );
++  else 
++    fixedauto = true;
++  // Set up mobile region
++  if (mobile_!=NULL)
++    mobileList_ = SetupAtomRanges( mobile_ );
++  else
++    mobileauto = true;
++  // Automatic search through molecules for fixed/mobile
++  if (fixedauto || mobileauto) {
++    int firstAtom = 0;
++    int lastAtom = 0;
++    for (int molnum = 0; molnum < currentParm->Nmol(); ++molnum)
++    {
++      firstAtom = lastAtom;
++      lastAtom += AtomsPerMol[ molnum ];
++      // Skip the anchor molecule
++      if (molnum != anchormolnum) { 
++        // Solvent and 1 atom molecules (prob. ions) go in mobile list,
++        // everything else into fixed list.
++        bool isSolventMol = false;
++        if ( currentParm->solventMask != NULL && currentParm->solventMask[firstAtom] == 'T' )
++          isSolventMol = true;
++        if ( isSolventMol || (lastAtom - firstAtom) == 1 ) 
++        {
++          if (mobileauto) {
++            mobileList_.push_back( firstAtom );
++            mobileList_.push_back( lastAtom  );
++          }
++        } else {
++          if (fixedauto) {
++            fixedList_.push_back( firstAtom );
++            fixedList_.push_back( lastAtom  );
++          }
++        }
++      }
++    }
++  }
++  // DEBUG: Print fixed and mobile lists
++  if (!fixedList_.empty()) {
++    mprintf("\tThe following molecules are fixed to anchor:");
++    for (pairList::iterator atom = fixedList_.begin(); 
++                            atom != fixedList_.end(); atom += 2)
++      mprintf(" %i", currentParm->atomToMolecule( *atom ) + 1 );
++    mprintf("\n");
++  }
++  mprintf("\t%zu molecules are mobile.\n", mobileList_.size() / 2 );
++  //mprintf("\tThe following molecules are mobile:\n");
++  //for (pairList::iterator atom = mobileList_.begin(); 
++  //                        atom != mobileList_.end(); atom += 2)
++  //  mprintf("\t\t%i\n", (*currentParm)[ *atom ].Mol()+1 );
++
++  truncoct_ = (triclinic_==FAMILIAR);
++
++  return 0;
++}
++
++// Action_AutoImage::action()
++int Action_AutoImage::action() {
++  double center[3], ucell[9], recip[9], imagedcenter[3], framecenter[3];
++  double fcom[3];
++  double bp[3], bm[3];
++  double Trans[3];
++
++  // Center w.r.t. anchor
++  currentFrame->Center( anchorMask_, origin_, useMass);
++  // Determine whether anchor center is at box center or coordinate origin
++  if (origin_) {
++    center[0] = 0;
++    center[1] = 0;
++    center[2] = 0;
++  } else {
++    center[0] = currentFrame->box[0] / 2;
++    center[1] = currentFrame->box[1] / 2;
++    center[2] = currentFrame->box[2] / 2;
++  }
++
++  // Setup imaging, and image everything in currentFrame 
++  // according to mobileList. 
++  if (ortho_) {
++    currentFrame->SetupImageOrtho(bp, bm, origin_);
++    currentFrame->ImageOrtho(bp, bm, center_, useMass, mobileList_);
++  } else {
++    currentFrame->BoxToRecip(ucell, recip);
++    if (truncoct_)
++      currentFrame->SetupImageTruncoct( fcom, NULL, useMass, origin_ );
++    currentFrame->ImageNonortho(origin_, fcom, ucell, recip, truncoct_,
++                                center_, useMass, mobileList_);
++  }  
++
++  // For each molecule defined by atom pairs in fixedList, determine if the
++  // imaged position is closer to anchor center than the current position.
++  // Always use molecule center when imaging fixedList.
++  for (pairList::iterator atom1 = fixedList_.begin();
++                          atom1 != fixedList_.end(); ++atom1)
++  {
++    int firstAtom = *atom1;
++    ++atom1;
++    int lastAtom = *atom1;
++    Trans[0] = 0;
++    Trans[1] = 0;
++    Trans[2] = 0;
++    if (useMass) 
++      currentFrame->CenterOfMass(framecenter, firstAtom, lastAtom);
++    else
++      currentFrame->GeometricCenter(framecenter, firstAtom, lastAtom);
++    // NOTE: imaging routines will modify input coords.
++    imagedcenter[0] = framecenter[0];
++    imagedcenter[1] = framecenter[1];
++    imagedcenter[2] = framecenter[2];
++    if (ortho_)
++      currentFrame->ImageOrtho(Trans, imagedcenter, bp, bm);
++    else
++      currentFrame->ImageNonortho(Trans, imagedcenter, truncoct_, origin_, ucell, recip, fcom);
++    // If molecule was imaged, determine whether imaged position is closer to anchor.
++    if (Trans[0] != 0 || Trans[1] != 0 || Trans[2] != 0) {
++      imagedcenter[0] = framecenter[0] + Trans[0];
++      imagedcenter[1] = framecenter[1] + Trans[1];
++      imagedcenter[2] = framecenter[2] + Trans[2];
++      double framedist2 = DIST2_NoImage( center, framecenter );
++      double imageddist2 = DIST2_NoImage( center, imagedcenter );
++      //mprintf("DBG: [%5i] Fixed @%i-%i frame dist2=%lf, imaged dist2=%lf\n", frameNum,
++      //        firstAtom+1, lastAtom+1,
++      //        framedist2, imageddist2);
++      if (imageddist2 < framedist2) {
++        // Imaging these atoms moved them closer to anchor. Update coords in currentFrame.
++        currentFrame->Translate(Trans, firstAtom, lastAtom);
++        //for (int idx = firstAtom*3; idx < lastAtom*3; ++idx)
++        //  (*currentFrame)[idx] = fixedFrame[idx];
++      }
++    }
++  }
++    
++  return 0;
++}
++
+diff --git a/AmberTools/src/cpptraj/src/Action_AutoImage.h b/AmberTools/src/cpptraj/src/Action_AutoImage.h
+index e69de29..5ee24d6 100644
+--- a/AmberTools/src/cpptraj/src/Action_AutoImage.h
++++ b/AmberTools/src/cpptraj/src/Action_AutoImage.h
+@@ -0,0 +1,32 @@
++#ifndef INC_ACTION_AUTOIMAGE_H
++#define INC_ACTION_AUTOIMAGE_H
++#include "Action.h"
++class Action_AutoImage : public Action {
++  public:
++    Action_AutoImage();
++
++  private:
++    int init();
++    int setup();
++    int action();
++
++    AtomMask anchorMask_; ///< Used to center anchor region.
++    char* anchor_;  ///< Mask expression for anchor region.
++    char* fixed_;   ///< Mask expression for fixed region.
++    char* mobile_;  ///< Mask expression for mobile region.
++
++    bool origin_;         ///< If true imaging occurs w.r.t. coordinate origin.
++    bool ortho_;          ///< If true imaging is orthogonal.
++    bool center_;         ///< If true imaging of mobile region uses molecule center.
++    bool truncoct_;
++    enum TriclinicArg {OFF, FORCE, FAMILIAR};
++    TriclinicArg triclinic_; ///< Determine whether triclinic code should be used.
++
++    typedef std::vector<int> pairList;
++    pairList anchorList_;
++    pairList fixedList_;
++    pairList mobileList_;
++
++    pairList SetupAtomRanges(const char*);
++};
++#endif
+diff --git a/AmberTools/src/cpptraj/src/Action_Center.cpp b/AmberTools/src/cpptraj/src/Action_Center.cpp
+index a496a7f..cb841b8 100644
+--- a/AmberTools/src/cpptraj/src/Action_Center.cpp
++++ b/AmberTools/src/cpptraj/src/Action_Center.cpp
+@@ -68,14 +68,7 @@ int Center::setup() {
+   */
+ int Center::action() {
+ 
+-  // Set up box
+-  if (!origin) {
+-    box[0] = currentFrame->box[0] / 2.0;
+-    box[1] = currentFrame->box[1] / 2.0;
+-    box[2] = currentFrame->box[2] / 2.0;
+-  }
+-  
+-  currentFrame->Center(&Mask1, box, useMass);
++  currentFrame->Center(Mask1, origin, useMass);
+ 
+   return 0;
+ } 
+diff --git a/AmberTools/src/cpptraj/src/Action_Image.cpp b/AmberTools/src/cpptraj/src/Action_Image.cpp
+index 023b26a..5e1dec8 100644
+--- a/AmberTools/src/cpptraj/src/Action_Image.cpp
++++ b/AmberTools/src/cpptraj/src/Action_Image.cpp
+@@ -1,26 +1,26 @@
+-// Image 
+-#include <cmath> //for floor
++// Action_Image 
+ #include "Action_Image.h"
+-#include "DistRoutines.h"
+ #include "CpptrajStdio.h"
+ 
+ // CONSTRUCTOR
+-Image::Image() {
++Action_Image::Action_Image() :
++  ComMask_(NULL),
++  origin_(false),
++  center_(false),
++  ortho_(false),
++  truncoct_(false),
++  triclinic_(OFF)
++{
+   //fprintf(stderr,"Image Con\n");
+-  ComMask=NULL;
+-  origin = false;
+-  center = false;
+-  ortho = false;
+   useMass = true;
+-  triclinic = OFF;
+ } 
+ 
+ // DESTRUCTOR
+-Image::~Image() {
+-  if (ComMask!=NULL) delete ComMask;
++Action_Image::~Action_Image() {
++  if (ComMask_!=NULL) delete ComMask_;
+ }
+ 
+-// Image::init()
++// Action_Image::init()
+ /** Expected call: image [origin] [center] [triclinic | familiar [com <mask>]] <mask>  
+   * - origin: center at 0.0, 0.0, 0.0, otherwise center at box center.
+   * - center: Use center of mass for imaging, otherwise use first atom.
+@@ -33,86 +33,86 @@ Image::~Image() {
+ // Check order is:
+ //    1) Keywords
+ //    2) Masks
+-int Image::init() {
++int Action_Image::init() {
+   char *mask1;
+ 
+   // Get keywords
+-  origin = actionArgs.hasKey("origin");
+-  center = actionArgs.hasKey("center");
+-  if (actionArgs.hasKey("familiar")) triclinic = FAMILIAR;
+-  if (actionArgs.hasKey("triclinic")) triclinic = FORCE;
++  origin_ = actionArgs.hasKey("origin");
++  center_ = actionArgs.hasKey("center");
++  if (actionArgs.hasKey("familiar")) triclinic_ = FAMILIAR;
++  if (actionArgs.hasKey("triclinic")) triclinic_ = FORCE;
+ 
+   // Get Masks
+-  if (triclinic == FAMILIAR) {
++  if (triclinic_ == FAMILIAR) {
+     mask1 = actionArgs.getKeyString("com",NULL);
+     if (mask1!=NULL) {
+-      ComMask = new AtomMask();
+-      ComMask->SetMaskString(mask1);
++      ComMask_ = new AtomMask();
++      ComMask_->SetMaskString(mask1);
+     }
+   }
+   mask1 = actionArgs.getNextMask();
+-  Mask1.SetMaskString(mask1);
++  Mask1_.SetMaskString(mask1);
+   
+   mprintf("    IMAGE: To");
+-  if (origin)
++  if (origin_)
+     mprintf(" origin");
+   else
+     mprintf(" box center");
+   mprintf(" based on");
+-  if (center)
++  if (center_)
+     mprintf(" center of mass");
+   else
+     mprintf(" first atom position");
+-  mprintf(" using atoms in mask %s\n",Mask1.MaskString());
+-  if (triclinic == FORCE)
++  mprintf(" using atoms in mask %s\n",Mask1_.MaskString());
++  if (triclinic_ == FORCE)
+     mprintf( "           Triclinic On.\n");
+-  else if (triclinic == FAMILIAR) {
++  else if (triclinic_ == FAMILIAR) {
+     mprintf( "           Triclinic On, familiar shape");
+-    if (ComMask!=NULL) 
+-      mprintf( " centering on atoms in mask %s", ComMask->MaskString());
++    if (ComMask_!=NULL) 
++      mprintf( " centering on atoms in mask %s", ComMask_->MaskString());
+     mprintf(".\n");
+   }
+ 
+   return 0;
+ }
+ 
+-// Image::setup()
++// Action_Image::setup()
+ /** Set Imaging up for this parmtop. Get masks etc.
+   * currentParm is set in Action::Setup
+   */
+-int Image::setup() {
+-  atomPair apair;
++int Action_Image::setup() {
++  //atomPair apair;
+ 
+-  if ( currentParm->SetupCharMask( Mask1, activeReference ) ) return 1;
+-  if (Mask1.None()) {
++  if ( currentParm->SetupCharMask( Mask1_, activeReference ) ) return 1;
++  if (Mask1_.None()) {
+     mprintf("Warning: Image::setup: Mask contains 0 atoms.\n");
+     return 1;
+   }
+ 
+-  if (currentParm->boxType==NOBOX) {
++  if (currentParm->boxType == NOBOX) {
+     mprintf("Warning: Image::setup: Parm %s does not contain box information.\n",
+             currentParm->parmName);
+     return 1;
+   }
+ 
+-  ortho = false;  
+-  if (currentParm->boxType==ORTHO && triclinic==OFF) ortho=true;
++  ortho_ = false;  
++  if (currentParm->boxType == ORTHO && triclinic_==OFF) ortho_=true;
+ 
+   // If box is originally truncated oct and not forcing triclinic, 
+   // turn familiar on.
+-  if (AmberIfbox(currentParm->Box[5])==2 && triclinic!=FORCE && triclinic!=FAMILIAR) {
++  if ( AmberIfbox( currentParm->Box[4] ) == 2 && triclinic_!=FORCE && triclinic_!=FAMILIAR) {
+     mprintf("\tOriginal box is truncated octahedron, turning on 'familiar'.\n");
+-    triclinic=FAMILIAR;
++    triclinic_=FAMILIAR;
+   }
+ 
+-  if (triclinic == FAMILIAR) {
+-    if (ComMask!=NULL) {
+-      if ( currentParm->SetupIntegerMask( *ComMask, activeReference) ) return 1;
+-      if (ComMask->None()) {
++  if (triclinic_ == FAMILIAR) {
++    if (ComMask_!=NULL) {
++      if ( currentParm->SetupIntegerMask( *ComMask_, activeReference ) ) return 1;
++      if (ComMask_->None()) {
+         mprintf("Warning: Image::setup: Mask for 'familiar com' contains no atoms.\n");
+         return 1;
+       }
+-      mprintf("\tcom: mask [%s] contains %i atoms.\n",ComMask->MaskString(),ComMask->Nselected);
++      mprintf("\tcom: mask [%s] contains %i atoms.\n",ComMask_->MaskString(),ComMask_->Nselected);
+     }
+   }
+ 
+@@ -120,178 +120,64 @@ int Image::setup() {
+   // Currently imaging by molecule only, so each pair will be the first and
+   // last atom of each molecule. Check that all atoms between first and last
+   // are actually in the mask.
+-  imageList.clear();
+-  imageList.reserve( currentParm->Nmol() );
+-  apair.firstAtom = 0;
+-  apair.lastAtom = 0;
+-  for (int mol = 0; mol < currentParm->Nmol(); mol++) {
+-    apair.firstAtom = apair.lastAtom;
+-    apair.lastAtom = apair.firstAtom + currentParm->AtomsPerMol(mol);
++  imageList_.clear();
++  imageList_.reserve( currentParm->Nmol() );
++  int* AtomsPerMol = currentParm->AtomsPerMol_ptr();
++  if (AtomsPerMol == NULL) {
++    mprinterr("Error: Image: No molecule information in %s\n", currentParm->parmName);
++    return 1;
++  } 
++  int firstAtom = 0;
++  int lastAtom = 0;
++  
++  for (int molnum = 0; molnum < currentParm->Nmol(); ++molnum) 
++  {
++    firstAtom = lastAtom;
++    lastAtom += AtomsPerMol[ molnum ];
+     // Check that each atom in the range is in Mask1
+     bool rangeIsValid = true;
+-    for (int atom = apair.firstAtom; atom < apair.lastAtom; atom++)
+-      if (!Mask1.AtomInCharMask(atom)) {rangeIsValid = false; break;}
+-    if (rangeIsValid) imageList.push_back( apair );
++    for (int atom = firstAtom; atom < lastAtom; atom++) {
++      if (!Mask1_.AtomInCharMask(atom)) {
++        rangeIsValid = false; 
++        break;
++      }
++    }
++    if (rangeIsValid) {
++      imageList_.push_back( firstAtom );
++      imageList_.push_back( lastAtom );
++    }
+   }
+-  mprintf("\tNumber of molecules to be imaged is %u based on mask [%s]\n", imageList.size(),
+-           Mask1.MaskString()); 
++  mprintf("\tNumber of molecules to be imaged is %u based on mask [%s]\n", imageList_.size()/2,
++           Mask1_.MaskString()); 
+   // DEBUG: Print all pairs
+-  //for (std::vector<atomPair>::iterator ap = imageList.begin();
+-  //                                     ap != imageList.end();
+-  //                                     ap++)
+-  //{
+-  //  mprintf("\tPair: %i - %i\n",(*ap).firstAtom+1,(*ap).lastAtom);
+-  //}
++  if (debug>0) {
++    for (std::vector<int>::iterator ap = imageList_.begin();
++                                    ap != imageList_.end(); ap+=2)
++      mprintf("\t\tMol First-Last atom#: %i - %i\n", (*ap)+1, *(ap+1) );
++  }
++
++  // Truncoct flag
++  truncoct_ = (triclinic_==FAMILIAR);
+ 
+   return 0;  
+ }
+ 
+-// Image::action()
+-int Image::action() {
+-  // Orthorhombic
+-  double bp[3];
+-  double bm[3];
+-  // Non-orthorhombic
+-  double ucell[9];
+-  double recip[9];
+-  double fc[3], ffc[3];
+-  // Familiar
+-  double fcom[3];
+-  int ixyz[3];
+-  // General
+-  double boxTrans[3];
+-  double Coord[3];
+-
+-  // Set up information for orthorhombic cell
+-  if (ortho) {
+-    if ( origin ) {
+-      bp[0] = currentFrame->box[0] / 2.0;
+-      bp[1] = currentFrame->box[1] / 2.0;
+-      bp[2] = currentFrame->box[2] / 2.0;
+-      bm[0] = -bp[0]; 
+-      bm[1] = -bp[1];
+-      bm[2] = -bp[2]; 
+-    } else {
+-      bp[0] = currentFrame->box[0];
+-      bp[1] = currentFrame->box[1];
+-      bp[2] = currentFrame->box[2];
+-      bm[0] = 0.0;
+-      bm[1] = 0.0; 
+-      bm[2] = 0.0; 
+-    }
+-
+-  // Set up information for non-orthorhombic cell
++// Action_Image::action()
++int Action_Image::action() {
++  // Ortho
++  double bp[3], bm[3];
++  // Nonortho
++  double ucell[9], recip[9], fcom[3];
++  
++  if (ortho_) {
++    currentFrame->SetupImageOrtho(bp, bm, origin_);
++    currentFrame->ImageOrtho(bp, bm, center_, useMass, imageList_);
+   } else {
+-    // NOTE: Does this need to be done every time?
+-    currentFrame->BoxToRecip(ucell, recip);
+-    // Set up centering if putting nonortho cell into familiar trunc. oct. shape
+-    if (triclinic == FAMILIAR) {
+-      // Use center of mask of atoms in mask
+-      if (ComMask!=NULL) {
+-        if (useMass)
+-          currentFrame->CenterOfMass(ComMask, fcom);
+-        else
+-          currentFrame->GeometricCenter(ComMask,fcom);
+-      // Use origin
+-      } else if (origin) {
+-        fcom[0]=0.0;
+-        fcom[1]=0.0;
+-        fcom[2]=0.0;
+-      // Use box center
+-      } else {
+-        fcom[0]=currentFrame->box[0] / 2.0; 
+-        fcom[1]=currentFrame->box[1] / 2.0; 
+-        fcom[2]=currentFrame->box[2] / 2.0;
+-      }
+-      //fprintf(stdout,"DEBUG: fcom = %lf %lf %lf\n",fcom[0],fcom[1],fcom[2]);
+-    } 
++    currentFrame->BoxToRecip( ucell, recip );
++    if (truncoct_)
++      currentFrame->SetupImageTruncoct( fcom, ComMask_, useMass, origin_ );
++    currentFrame->ImageNonortho(origin_, fcom, ucell, recip, truncoct_,
++                                center_, useMass, imageList_);
+   }
+-
+-  // Loop over Atom pairs
+-  for (std::vector<atomPair>::iterator apair = imageList.begin();
+-                                       apair != imageList.end();
+-                                       apair++)
+-  {
+-    int firstAtom = (*apair).firstAtom;
+-    int lastAtom  = (*apair).lastAtom;
+-
+-    //if (debug>2)
+-    //  mprintf( "  IMAGE processing atoms %i to %i\n", firstAtom+1, lastAtom); 
+-
+-    // boxTrans will hold calculated translation needed to move atoms back into box
+-    boxTrans[0] = 0.0;
+-    boxTrans[1] = 0.0;
+-    boxTrans[2] = 0.0;
+-
+-    // Set up position based on first atom or center of mass
+-    if (center) { 
+-      if (useMass)
+-        currentFrame->CenterOfMass(Coord,firstAtom,lastAtom);
+-      else
+-        currentFrame->GeometricCenter(Coord,firstAtom,lastAtom);
+-    } else
+-      currentFrame->GetCoord(Coord,firstAtom);
+-
+-    // ORTHORHOMBIC
+-    if (ortho) {
+-      // Determine how far coords are out of box
+-      for (int i=0; i<3; i++) {
+-        while (Coord[i] < bm[i]) {
+-          Coord[i] += currentFrame->box[i];
+-          boxTrans[i] += currentFrame->box[i];
+-        }
+-        while (Coord[i] > bp[i]) {
+-          Coord[i] -= currentFrame->box[i];
+-          boxTrans[i] -= currentFrame->box[i];
+-        }
+-      }
+-
+-    // NON-ORTHORHOMBIC    
+-    } else {
+-      fc[0]=(Coord[0]*recip[0]) + (Coord[1]*recip[1]) + (Coord[2]*recip[2]);
+-      fc[1]=(Coord[0]*recip[3]) + (Coord[1]*recip[4]) + (Coord[2]*recip[5]);
+-      fc[2]=(Coord[0]*recip[6]) + (Coord[1]*recip[7]) + (Coord[2]*recip[8]);
+-
+-      if ( origin ) {
+-        fc[0] += 0.5;
+-        fc[1] += 0.5;
+-        fc[2] += 0.5;
+-      }
+-
+-      ffc[0] = floor(fc[0]);
+-      ffc[1] = floor(fc[1]);
+-      ffc[2] = floor(fc[2]);
+-
+-      boxTrans[0] -= (ffc[0]*ucell[0] + ffc[1]*ucell[3] + ffc[2]*ucell[6]);
+-      boxTrans[1] -= (ffc[0]*ucell[1] + ffc[1]*ucell[4] + ffc[2]*ucell[7]);
+-      boxTrans[2] -= (ffc[0]*ucell[2] + ffc[1]*ucell[5] + ffc[2]*ucell[8]);
+-
+-      // Put into familiar trunc. oct. shape
+-      if (triclinic == FAMILIAR) {
+-        Coord[0] += boxTrans[0];
+-        Coord[1] += boxTrans[1];
+-        Coord[2] += boxTrans[2];
+-        MinImageNonOrtho2(Coord, fcom, currentFrame->box, (int)origin, ixyz, ucell, recip);
+-        if (ixyz[0] != 0 || ixyz[1] != 0 || ixyz[2] != 0) {
+-          boxTrans[0] += (ixyz[0]*ucell[0] + ixyz[1]*ucell[3] + ixyz[2]*ucell[6]);
+-          boxTrans[1] += (ixyz[0]*ucell[1] + ixyz[1]*ucell[4] + ixyz[2]*ucell[7]);
+-          boxTrans[2] += (ixyz[0]*ucell[2] + ixyz[1]*ucell[5] + ixyz[2]*ucell[8]);
+-
+-          //if (debug > 2)
+-          //  mprintf( "  IMAGING, FAMILIAR OFFSETS ARE %i %i %i\n", 
+-          //          ixyz[0], ixyz[1], ixyz[2]);
+-        }
+-      }  
+-    }    
+-   
+-    //fprintf(stdout,"DEBUG: BoxTrans: %lf %lf %lf\n",boxTrans[0],boxTrans[1],boxTrans[2]);
+-
+-    // Translate atoms back into the box
+-    currentFrame->Translate(boxTrans,firstAtom,lastAtom);
+-
+-  } // END loop over atom pairs 
+-
+   return 0;
+ } 
+-
+-
+diff --git a/AmberTools/src/cpptraj/src/Action_Image.h b/AmberTools/src/cpptraj/src/Action_Image.h
+index ba233c1..139246e 100644
+--- a/AmberTools/src/cpptraj/src/Action_Image.h
++++ b/AmberTools/src/cpptraj/src/Action_Image.h
+@@ -1,31 +1,28 @@
+ #ifndef INC_ACTION_IMAGE_H
+ #define INC_ACTION_IMAGE_H
+-// Class: Image
++// Class: Action_Image
+ /// Action to wrap coordinates back into primary box
+ #include "Action.h"
+-class Image: public Action {
++class Action_Image: public Action {
++  public:
++    Action_Image();
++    ~Action_Image();
++  private:
+     /// Only atoms in Mask1 will be imaged
+-    AtomMask Mask1;
++    AtomMask Mask1_;
+     /// If defined, image w.r.t. the center of atoms in ComMask.
+-    AtomMask *ComMask;
++    AtomMask *ComMask_;
+     /// If true image w.r.t. coordinate origin, otherwise box center
+-    bool origin;
++    bool origin_;
+     /// If true molecules will be imaged w.r.t. their center, otherwise first atom will be used
+-    bool center;
++    bool center_;
+     /// True if orthorhombic cell, false otherwise.
+-    bool ortho;
++    bool ortho_;
++    bool truncoct_;
+     enum TriclinicArg {OFF, FORCE, FAMILIAR};
+-    TriclinicArg triclinic;
+-    struct atomPair {
+-      int firstAtom;
+-      int lastAtom;
+-    };
++    TriclinicArg triclinic_;
+     /// Vector containing atom ranges to be imaged (first to last)
+-    std::vector<atomPair> imageList; 
+-
+-  public:
+-    Image();
+-    ~Image();
++    std::vector<int> imageList_; 
+ 
+     int init();
+     int setup();
+diff --git a/AmberTools/src/cpptraj/src/CpptrajState.cpp b/AmberTools/src/cpptraj/src/CpptrajState.cpp
+index 7aa0e9e..4ce4228 100644
+--- a/AmberTools/src/cpptraj/src/CpptrajState.cpp
++++ b/AmberTools/src/cpptraj/src/CpptrajState.cpp
+@@ -209,11 +209,16 @@ int CpptrajState::Run() {
+     }
+     // Set current parm from current traj.
+     CurrentParm = traj->TrajParm();
++    // Check if parm has changed
++    bool parmHasChanged = (lastPindex != CurrentParm->pindex);
+ 
+-    // If Parm has changed, reset Frame and actions for new topology.
+-    if (lastPindex != CurrentParm->pindex) {
+-      // Set up the incoming trajectory frame for this parm
++    // If Parm has changed or trajectory velocity status has changed,
++    // reset the frame.
++    if (parmHasChanged || ((TrajFrame.V != NULL) != traj->HasVelocity()))
+       TrajFrame.SetupFrameV(CurrentParm->natom, CurrentParm->mass, traj->HasVelocity());
++
++    // If Parm has changed, reset actions for new topology.
++    if (parmHasChanged) {
+       // Set up actions for this parm
+       if (actionList.Setup( &CurrentParm )) {
+         mprintf("WARNING: Could not set up actions for %s: skipping.\n",
+diff --git a/AmberTools/src/cpptraj/src/Frame.cpp b/AmberTools/src/cpptraj/src/Frame.cpp
+index 3a8add6..0adbe67 100644
+--- a/AmberTools/src/cpptraj/src/Frame.cpp
++++ b/AmberTools/src/cpptraj/src/Frame.cpp
+@@ -462,20 +462,29 @@ void Frame::InverseRotate(double *T) {
+   * or box center. Use geometric center if mass is NULL, otherwise center 
+   * of mass will be used.
+   */
+-void Frame::Center(AtomMask *Mask, double *boxcoord, bool useMassIn) {
++void Frame::Center(AtomMask& Mask, bool origin, bool useMassIn) {
+   double center[3];
+ 
+   if (useMassIn)
+-    this->CenterOfMass(Mask, center);
++    this->CenterOfMass(&Mask, center);
+   else
+-    this->GeometricCenter(Mask, center);
++    this->GeometricCenter(&Mask, center);
+   //mprinterr("  FRAME CENTER: %lf %lf %lf\n",center[0],center[1],center[2]); //DEBUG
+ 
+-  // Shift to whatever is in boxcoord (origin or center of box in Action_Center) 
+-  center[0] = boxcoord[0] - center[0]; 
+-  center[1] = boxcoord[1] - center[1]; 
+-  center[2] = boxcoord[2] - center[2];
++  if (origin) {
++    // Shift to coordinate origin (0,0,0)
++    center[0] = -center[0];
++    center[1] = -center[1];
++    center[2] = -center[2];
++  } else {
++    // Shift to box center
++    center[0] = (box[0] / 2) - center[0];
++    center[1] = (box[1] / 2) - center[1];
++    center[2] = (box[2] / 2) - center[2];
++  }
++
+   this->Translate(center);
++
+ }
+ 
+ // Frame::CenterReference()
+@@ -510,6 +519,202 @@ void Frame::ShiftToGeometricCenter( ) {
+   this->Translate(frameCOM);
+ }
+ 
++void Frame::SetupImageTruncoct( double* fcom, AtomMask* ComMask, bool useMass, bool origin )
++{
++  // Set up centering if putting nonortho cell into familiar trunc. oct. shape
++  //if (truncoct) {
++    if (ComMask!=NULL) {
++      // Use center of atoms in mask
++      if (useMass)
++        CenterOfMass(ComMask, fcom);
++      else
++        GeometricCenter(ComMask, fcom);
++    } else if (origin) {
++      // Use origin
++      fcom[0] = 0;
++      fcom[1] = 0;
++      fcom[2] = 0;
++    } else {
++      // Use box center
++      fcom[0] = box[0] / 2;
++      fcom[1] = box[1] / 2;
++      fcom[2] = box[2] / 2;
++    }
++    //fprintf(stdout,"DEBUG: fcom = %lf %lf %lf\n",fcom[0],fcom[1],fcom[2]);
++  //}
++}
++
++// Frame::ImageNonortho()
++void Frame::ImageNonortho(bool origin, double* fcom, double* ucell, double* recip,
++                          bool truncoct, bool center,
++                          bool useMass, std::vector<int> &AtomPairs)
++{
++  //double ucell[9], recip[9], 
++  double boxTrans[3], Coord[3];
++  // fcom and ixyz only needed for truncoct
++  //double fcom[3];
++
++  //BoxToRecip(ucell, recip);
++
++  // Loop over atom pairs
++  for (std::vector<int>::iterator atom = AtomPairs.begin();
++                                  atom != AtomPairs.end();
++                                  atom++)
++  {
++    int firstAtom = *atom;
++    ++atom;
++    int lastAtom = *atom;
++    //if (debug>2)
++    //  mprintf( "  IMAGE processing atoms %i to %i\n", firstAtom+1, lastAtom);
++    // boxTrans will hold calculated translation needed to move atoms back into box
++    boxTrans[0] = 0;
++    boxTrans[1] = 0;
++    boxTrans[2] = 0;
++    // Set up Coord with position to check for imaging based on first atom or 
++    // center of mass of atoms first to last.
++    if (center) {
++      if (useMass)
++        CenterOfMass(Coord,firstAtom,lastAtom);
++      else
++        GeometricCenter(Coord,firstAtom,lastAtom);
++    } else {
++      int atomidx = firstAtom * 3;
++      Coord[0] = X[atomidx];
++      ++atomidx;
++      Coord[1] = X[atomidx];
++      ++atomidx;
++      Coord[2] = X[atomidx];
++    }
++
++    ImageNonortho(boxTrans, Coord, truncoct, origin,
++                  ucell, recip, fcom);
++
++    Translate(boxTrans, firstAtom, lastAtom);
++
++  } // END loop over atom pairs
++}
++
++// Frame::ImageNonortho()
++void Frame::ImageNonortho(double* boxTrans, double* Coord,
++                          bool truncoct, bool origin,
++                          double* ucell, double* recip, double* fcom)
++{
++  double fc[3], ffc[3];
++  int ixyz[3];
++
++  fc[0]=(Coord[0]*recip[0]) + (Coord[1]*recip[1]) + (Coord[2]*recip[2]);
++  fc[1]=(Coord[0]*recip[3]) + (Coord[1]*recip[4]) + (Coord[2]*recip[5]);
++  fc[2]=(Coord[0]*recip[6]) + (Coord[1]*recip[7]) + (Coord[2]*recip[8]);
++
++  if ( origin ) {
++    fc[0] += 0.5;
++    fc[1] += 0.5;
++    fc[2] += 0.5;
++  }
++
++  ffc[0] = floor(fc[0]);
++  ffc[1] = floor(fc[1]);
++  ffc[2] = floor(fc[2]);
++
++  boxTrans[0] -= (ffc[0]*ucell[0] + ffc[1]*ucell[3] + ffc[2]*ucell[6]);
++  boxTrans[1] -= (ffc[0]*ucell[1] + ffc[1]*ucell[4] + ffc[2]*ucell[7]);
++  boxTrans[2] -= (ffc[0]*ucell[2] + ffc[1]*ucell[5] + ffc[2]*ucell[8]);
++
++  // Put into familiar trunc. oct. shape
++  if (truncoct) {
++    Coord[0] += boxTrans[0];
++    Coord[1] += boxTrans[1];
++    Coord[2] += boxTrans[2];
++    MinImageNonOrtho2(Coord, fcom, box, (int)origin, ixyz, ucell, recip);
++    if (ixyz[0] != 0 || ixyz[1] != 0 || ixyz[2] != 0) {
++      boxTrans[0] += (ixyz[0]*ucell[0] + ixyz[1]*ucell[3] + ixyz[2]*ucell[6]);
++      boxTrans[1] += (ixyz[0]*ucell[1] + ixyz[1]*ucell[4] + ixyz[2]*ucell[7]);
++      boxTrans[2] += (ixyz[0]*ucell[2] + ixyz[1]*ucell[5] + ixyz[2]*ucell[8]);
++
++      //if (debug > 2)
++      //  mprintf( "  IMAGING, FAMILIAR OFFSETS ARE %i %i %i\n", 
++      //          ixyz[0], ixyz[1], ixyz[2]);
++    }
++  }
++}
++
++void Frame::SetupImageOrtho(double* bp, double* bm, bool origin) {
++  // Set up boundary information for orthorhombic cell
++  if (origin) {
++    bp[0] = box[0] / 2;
++    bp[1] = box[1] / 2;
++    bp[2] = box[2] / 2;
++    bm[0] = -bp[0];
++    bm[1] = -bp[1];
++    bm[2] = -bp[2];
++  } else {
++    bp[0] = box[0];
++    bp[1] = box[1];
++    bp[2] = box[2];
++    bm[0] = 0;
++    bm[1] = 0;
++    bm[2] = 0;
++  }
++}
++
++// Frame::ImageOrtho()
++void Frame::ImageOrtho(double* bp, double* bm, bool center, bool useMass,
++                       std::vector<int> &AtomPairs)
++{
++  double boxTrans[3], Coord[3];
++
++  // Loop over atom pairs
++  for (std::vector<int>::iterator atom = AtomPairs.begin();
++                                  atom != AtomPairs.end();
++                                  atom++)
++  {
++    int firstAtom = *atom;
++    ++atom;
++    int lastAtom = *atom;
++    //if (debug>2)
++    //  mprintf( "  IMAGE processing atoms %i to %i\n", firstAtom+1, lastAtom);
++    // boxTrans will hold calculated translation needed to move atoms back into box
++    boxTrans[0] = 0;
++    boxTrans[1] = 0;
++    boxTrans[2] = 0;
++    // Set up Coord with position to check for imaging based on first atom or 
++    // center of mass of atoms first to last.
++    if (center) {
++      if (useMass)
++        CenterOfMass(Coord,firstAtom,lastAtom);
++      else
++        GeometricCenter(Coord,firstAtom,lastAtom);
++    } else {
++      int atomidx = firstAtom * 3;
++      Coord[0] = X[atomidx];
++      ++atomidx;
++      Coord[1] = X[atomidx];
++      ++atomidx;
++      Coord[2] = X[atomidx];
++    }
++    ImageOrtho(boxTrans, Coord,bp,bm);
++
++    // Translate atoms according to Coord
++    Translate(boxTrans,firstAtom,lastAtom);
++  } // END loop over atom pairs
++}
++
++void Frame::ImageOrtho(double* boxTrans, double* Coord, double* bp, double* bm)
++{
++    // Determine how far Coord is out of box
++    for (int i=0; i < 3; i++) {
++      while (Coord[i] < bm[i]) {
++        Coord[i] += box[i];
++        boxTrans[i] += box[i];
++      }
++      while (Coord[i] > bp[i]) {
++        Coord[i] -= box[i];
++        boxTrans[i] -= box[i];
++      }
++    }
++}
++
++
+ /* -------------- Coordinate Assignment/Extraction Routines ----------------- */
+ // Frame::printAtomCoord()
+ /** Print XYZ coords of given atom */
+diff --git a/AmberTools/src/cpptraj/src/Frame.h b/AmberTools/src/cpptraj/src/Frame.h
+index fb9be8b..b24f86c 100644
+--- a/AmberTools/src/cpptraj/src/Frame.h
++++ b/AmberTools/src/cpptraj/src/Frame.h
+@@ -53,9 +53,15 @@ class Frame {
+     void Trans_Rot_Trans(double *, double *);
+     void Rotate(double *);
+     void InverseRotate(double *);
+-    void Center(AtomMask *, double *,bool);
++    void Center(AtomMask&, bool,bool);
+     void CenterReference(double *, bool);
+     void ShiftToGeometricCenter();
++    void SetupImageTruncoct(double*, AtomMask*,bool,bool);
++    void ImageNonortho(bool, double*, double*, double*, bool, bool, bool, std::vector<int> &);
++    void ImageNonortho(double*, double*, bool, bool, double*, double*, double*);
++    void SetupImageOrtho(double*, double*, bool);
++    void ImageOrtho(double*,double*, bool, bool, std::vector<int> &);
++    void ImageOrtho(double*, double*, double*, double*);
+     // Coordinate assignment/extraction
+     void printAtomCoord(int);
+     void GetCoord(double *, int);
+diff --git a/AmberTools/src/cpptraj/src/Parm_CharmmPsf.cpp b/AmberTools/src/cpptraj/src/Parm_CharmmPsf.cpp
+index 98d1059..c11edc1 100644
+--- a/AmberTools/src/cpptraj/src/Parm_CharmmPsf.cpp
++++ b/AmberTools/src/cpptraj/src/Parm_CharmmPsf.cpp
+@@ -14,7 +14,7 @@ int CharmmPsfParmFile::ReadParm(AmberParm &parmOut, CpptrajFile &parmfile) {
+   int bondatoms[8];
+   int currResnum;
+   int psfresnum;
+-  int psfattype;
++  char psfattype[6];
+   int nbond,nlines;
+ 
+   mprintf("    Reading Charmm PSF file %s as topology file.\n",parmOut.parmName);
+@@ -58,8 +58,8 @@ int CharmmPsfParmFile::ReadParm(AmberParm &parmOut, CpptrajFile &parmfile) {
+     //if (buffer[bufferLen-1] == '\n') buffer[bufferLen-1]='\0';
+     // Read line
+     // ATOM# SEGID RES# RES ATNAME ATTYPE CHRG MASS (REST OF COLUMNS ARE LIKELY FOR CMAP AND CHEQ)
+-    sscanf(buffer,"%*i %*s %i %s %s %i %lf %lf",&psfresnum,psfresname,psfname,
+-           &psfattype,parmOut.charge+atom,parmOut.mass+atom);
++    sscanf(buffer,"%*i %*s %i %s %s %s %lf %lf",&psfresnum,psfresname,psfname,
++           psfattype,parmOut.charge+atom,parmOut.mass+atom);
+     // Ensure name has 4 chars
+     PadWithSpaces( psfname );
+     strcpy(parmOut.names[atom],psfname);
+diff --git a/AmberTools/src/cpptraj/src/Traj_AmberRestart.cpp b/AmberTools/src/cpptraj/src/Traj_AmberRestart.cpp
+index d2a398a..6d060a6 100644
+--- a/AmberTools/src/cpptraj/src/Traj_AmberRestart.cpp
++++ b/AmberTools/src/cpptraj/src/Traj_AmberRestart.cpp
+@@ -9,6 +9,7 @@
+ // CONSTRUCTOR
+ AmberRestart::AmberRestart() {
+   restartAtoms=0;
++  coordSize_ = 0;
+   frameSize=0;
+   frameBuffer=NULL;
+   numBoxCoords=0;
+@@ -218,6 +219,7 @@ int AmberRestart::setupRead(AmberParm *trajParm) {
+   // For DOS files CR present before newline
+   if (tfile->isDos) frame_lines*=2;
+   frameSize = ((natom3 * 12) + frame_lines);
++  coordSize_ = frameSize;
+   frameBuffer=(char*) malloc(frameSize*sizeof(char));
+   //if (debug>0) mprintf("    Amber Restart frameSize= %i\n",frameSize);
+ 
+@@ -302,13 +304,16 @@ int AmberRestart::readFrame(int set,double *X,double *V,double *box, double *T)
+     return 1;  
+   }
+   // Get velocity from buffer if present
+-  if (hasVelocity && V!=NULL) {
+-    if ( (bufferPosition = BufferToDouble(bufferPosition, V, natom3, 12))==NULL ) {
+-      mprinterr("Error: AmberRestart::getFrame: * detected in velocities of %s\n",
+-              tfile->filename);
+-      return 1;
++  if (hasVelocity) {
++    if (V != NULL) {
++      if ( (bufferPosition = BufferToDouble(bufferPosition, V, natom3, 12))==NULL ) {
++        mprinterr("Error: AmberRestart::getFrame: * detected in velocities of %s\n",
++                tfile->filename);
++        return 1;
++      }
++    } else {
++      bufferPosition += coordSize_;
+     }
+-    //F->V->printAtomCoord(0);
+   }
+   // Get box from buffer if present
+   if (hasBox) {
+diff --git a/AmberTools/src/cpptraj/src/Traj_AmberRestart.h b/AmberTools/src/cpptraj/src/Traj_AmberRestart.h
+index ba21b2a..b231874 100644
+--- a/AmberTools/src/cpptraj/src/Traj_AmberRestart.h
++++ b/AmberTools/src/cpptraj/src/Traj_AmberRestart.h
+@@ -7,6 +7,7 @@ class AmberRestart : public TrajectoryIO {
+     int restartAtoms;     ///< Number of atoms in restart file
+     int natom3;           ///< Number of coords
+     int frameSize;        ///< Size of 1 coord frame in bytes, inc box & velo if present
++    size_t coordSize_;    ///< Size of 1 coord frame in bytes, used for blank reads.
+     char *frameBuffer;    ///< Used to read in restart coord
+     int numBoxCoords;     ///< Number of box coords (3 or 6)
+     double restartTime;   ///< Time in restart file, read in
+diff --git a/AmberTools/src/cpptraj/src/Traj_CharmmDcd.cpp b/AmberTools/src/cpptraj/src/Traj_CharmmDcd.cpp
+index 8563938..6074b05 100644
+--- a/AmberTools/src/cpptraj/src/Traj_CharmmDcd.cpp
++++ b/AmberTools/src/cpptraj/src/Traj_CharmmDcd.cpp
+@@ -203,7 +203,39 @@ int CharmmDcd::WriteBlock(int blocksize) {
+ /** Call openTraj, which reads the DCD header and all necessary info.
+   */
+ int CharmmDcd::setupRead(AmberParm *trajParm) {
++  size_t boxBytes, dim;
+   if ( openTraj() ) return -1;
++  // DCD file may have less frames than is stored in the header. 
++  // Check the file size against the reported number of frames.
++  if (hasBox)
++    boxBytes = 56; // 6(crds) * 8(double) + 4(hdr) + 4(end hdr)
++  else
++    boxBytes = 0;
++  if (dcd4D)
++    dim = 4;
++  else
++    dim = 3;
++  size_t dimBytes = dim * sizeof(float);
++  size_t frame1Bytes = (((size_t) dcdatom+2         ) * dimBytes) + boxBytes;
++  size_t frameNBytes = (((size_t)(dcdatom - namnf)+2) * dimBytes) + boxBytes;
++  // Header size should be current position after open, which automatically
++  // reads DCD header.
++  size_t headerBytes = (size_t)tfile->IO->Tell();
++  size_t file_size = (size_t)tfile->file_size - headerBytes - frame1Bytes;
++  if ( (file_size % frameNBytes) != 0 ) {
++    mprintf("Warning: %s: Number of frames in DCD file could not be accurately determined.\n",
++            tfile->filename);
++    mprintf("Warning:\t\tFile may be corrupted.\n");
++  }
++  int nframes = (int)(file_size / frameNBytes) + 1; // +1 for first frame
++  if (nframes != dcdframes) {
++    mprintf("Warning: %s: Reported number of frames in DCD file is %i,\n", 
++            tfile->filename, dcdframes);
++    mprintf("Warning:\tactual number of frames is %i. Only reading %i frames.\n",
++            nframes, nframes);
++    dcdframes = nframes;
++  }
++
+   closeTraj();
+   return dcdframes;
+ }
+diff --git a/AmberTools/src/cpptraj/src/TrajectoryFile.cpp b/AmberTools/src/cpptraj/src/TrajectoryFile.cpp
+index e51b442..1fb8d14 100644
+--- a/AmberTools/src/cpptraj/src/TrajectoryFile.cpp
++++ b/AmberTools/src/cpptraj/src/TrajectoryFile.cpp
+@@ -635,6 +635,7 @@ FileFormat TrajectoryFile::getFmtFromArg(ArgList *argIn, FileFormat def) {
+   else if ( argIn->hasKey("restartnc")) writeFormat=AMBERRESTARTNC;
+   else if ( argIn->hasKey("mol2")     ) writeFormat=MOL2FILE;
+   else if ( argIn->hasKey("dcd")      ) writeFormat=CHARMMDCD;
++  else if ( argIn->hasKey("charmm")   ) writeFormat=CHARMMDCD;
+   return writeFormat;
+ }
+ 
+diff --git a/AmberTools/src/cpptraj/src/cpptrajdepend b/AmberTools/src/cpptraj/src/cpptrajdepend
+index c8a9751..27016ab 100644
+--- a/AmberTools/src/cpptraj/src/cpptrajdepend
++++ b/AmberTools/src/cpptraj/src/cpptrajdepend
+@@ -38,13 +38,14 @@ Action_Center.o : Action_Center.cpp Action.h Action_Center.h AmberParm.h ArgList
+ FileIO_Bzip2.o : FileIO_Bzip2.cpp CpptrajStdio.h FileIO.h FileIO_Bzip2.h
+ Action_Hbond.o : Action_Hbond.cpp Action.h Action_Hbond.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h Constants.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h
+ DataSet_integer.o : DataSet_integer.cpp CharBuffer.h CpptrajStdio.h DataSet.h DataSet_integer.h MpiRoutines.h
+-Action_Image.o : Action_Image.cpp Action.h Action_Image.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DistRoutines.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h
++Action_Image.o : Action_Image.cpp Action.h Action_Image.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h
+ Action_Surf.o : Action_Surf.cpp Action.h Action_Surf.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h Constants.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h
+ Action_Radgyr.o : Action_Radgyr.cpp Action.h Action_Radgyr.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h
+ Action_Mask.o : Action_Mask.cpp Action.h Action_Mask.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h ProgressBar.h Range.h TrajectoryFile.h TrajectoryIO.h
+ Action_Closest.o : Action_Closest.cpp Action.h Action_Closest.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFile.h ParmFileList.h
+ NetcdfRoutines.o : NetcdfRoutines.cpp CpptrajStdio.h NetcdfRoutines.h
+ CpptrajStdio.o : CpptrajStdio.cpp MpiRoutines.h
++Action_AutoImage.o : Action_AutoImage.cpp Action.h Action_AutoImage.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DistRoutines.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h
+ Mol2FileRoutines.o : Mol2FileRoutines.cpp CharBuffer.h CpptrajFile.h CpptrajStdio.h FileIO.h FileRoutines.h Mol2FileRoutines.h Name.h
+ Action_NAstruct.o : Action_NAstruct.cpp Action.h Action_NAstruct.h AmberParm.h ArgList.h AtomMask.h AxisType.h Bonds.h BoxType.h CharBuffer.h Constants.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DistRoutines.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h Range.h vectormath.h
+ DistRoutines.o : DistRoutines.cpp Constants.h DistRoutines.h
+@@ -80,7 +81,7 @@ Action_Jcoupling.o : Action_Jcoupling.cpp Action.h Action_Jcoupling.h AmberParm.
+ TriangleMatrix.o : TriangleMatrix.cpp CpptrajStdio.h TriangleMatrix.h
+ Action_Clustering.o : Action_Clustering.cpp Action.h Action_Clustering.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h ClusterList.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h ProgressBar.h Range.h TrajectoryFile.h TrajectoryIO.h TriangleMatrix.h
+ ClusterList.o : ClusterList.cpp CharBuffer.h ClusterList.h CpptrajFile.h CpptrajStdio.h FileIO.h FileRoutines.h TriangleMatrix.h
+-Traj_CharmmDcd.o : Traj_CharmmDcd.cpp AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h CpptrajFile.h CpptrajStdio.h FileIO.h FileRoutines.h Name.h Traj_CharmmDcd.h TrajectoryIO.h
++Traj_CharmmDcd.o : Traj_CharmmDcd.cpp AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileRoutines.h Name.h Traj_CharmmDcd.h TrajectoryIO.h
+ Bonds.o : Bonds.cpp Bonds.h CpptrajStdio.h Name.h
+ FileRoutines.o : FileRoutines.cpp FileRoutines.h
+ Action_Pairwise.o : Action_Pairwise.cpp Action.h Action_Pairwise.h AmberParm.h ArgList.h AtomMask.h Bonds.h BoxType.h CharBuffer.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h FileIO.h FileRoutines.h Frame.h FrameList.h Name.h ParmFileList.h ProgressBar.h Range.h TrajectoryFile.h TrajectoryIO.h vectormath.h
+diff --git a/AmberTools/src/cpptraj/src/cpptrajfiles b/AmberTools/src/cpptraj/src/cpptrajfiles
+index f7ecc50..9c05282 100644
+--- a/AmberTools/src/cpptraj/src/cpptrajfiles
++++ b/AmberTools/src/cpptraj/src/cpptrajfiles
+@@ -10,7 +10,7 @@ SOURCE=main.cpp AmberParm.cpp \
+        Action_DSSP.cpp DataSet_string.cpp Action_Center.cpp FileIO_Bzip2.cpp \
+        Action_Hbond.cpp DataSet_integer.cpp Action_Image.cpp Action_Surf.cpp \
+        Action_Radgyr.cpp Action_Mask.cpp Action_Closest.cpp \
+-       NetcdfRoutines.cpp CpptrajStdio.cpp \
++       NetcdfRoutines.cpp CpptrajStdio.cpp Action_AutoImage.cpp \
+        Mol2FileRoutines.cpp Action_NAstruct.cpp DistRoutines.cpp AxisType.cpp \
+        TorsionRoutines.cpp Action_Pucker.cpp Range.cpp Action_Outtraj.cpp \
+        Action_Rms2d.cpp ProgressBar.cpp TrajectoryIO.cpp \
+@@ -42,7 +42,7 @@ OBJECTS=main.o AmberParm.o \
+         Action_DSSP.o DataSet_string.o Action_Center.o FileIO_Bzip2.o \
+         Action_Hbond.o DataSet_integer.o Action_Image.o Action_Surf.o \
+         Action_Radgyr.o Action_Mask.o Action_Closest.o \
+-        NetcdfRoutines.o CpptrajStdio.o \
++        NetcdfRoutines.o CpptrajStdio.o Action_AutoImage.o \
+         Mol2FileRoutines.o Action_NAstruct.o DistRoutines.o AxisType.o \
+         TorsionRoutines.o Action_Pucker.o Range.o Action_Outtraj.o \
+         Action_Rms2d.o ProgressBar.o TrajectoryIO.o \
+@@ -74,7 +74,7 @@ HEADERS=AmberParm.h \
+         Action_DSSP.h DataSet_string.h Action_Center.h FileIO_Bzip2.h \
+         Action_Hbond.h DataSet_integer.h Action_Image.h Action_Surf.h \
+         Action_Radgyr.h Action_Mask.h Action_Closest.h \
+-        NetcdfRoutines.h CpptrajStdio.h \
++        NetcdfRoutines.h CpptrajStdio.h Action_AutoImage.h \
+         Mol2FileRoutines.h Action_NAstruct.h DistRoutines.h AxisType.h \
+         TorsionRoutines.h Action_Pucker.h Range.h Action_Outtraj.h \
+         Action_Rms2d.h ProgressBar.h TrajectoryIO.h \
+diff --git a/AmberTools/src/cpptraj/src/main.cpp b/AmberTools/src/cpptraj/src/main.cpp
+index 23f290e..4fc0434 100644
+--- a/AmberTools/src/cpptraj/src/main.cpp
++++ b/AmberTools/src/cpptraj/src/main.cpp
+@@ -9,7 +9,7 @@
+ #include <cstdio>
+ #include <cstdlib> // atoi
+ #ifndef CPPTRAJ_VERSION_STRING
+-#define CPPTRAJ_VERSION_STRING "V12.1"
++#define CPPTRAJ_VERSION_STRING "V12.4"
+ #define CPPTRAJ_INTERNAL_VERSION "V2.4.7b"
+ #endif
+ 
+diff --git a/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py b/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py
+index b01b891..0349ba9 100644
+--- a/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py
++++ b/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py
+@@ -1152,7 +1152,7 @@ class BindingStatistics(object):
+       classes and returns the average and standard deviation of that diff.
+       """
+       if len(self.data[key1]) != len(other.data[key2]):
+-         return (self.data[key1].avg() - self.data[key2].avg(),
++         return (self.data[key1].avg() - other.data[key2].avg(),
+                  sqrt(self.data[key1].stdev()**2 + other.data[key2].stdev()**2))
+       
+       mydiff = self.data[key1] - other.data[key2]
+diff --git a/AmberTools/src/mmpbsa_py/MMPBSA_mods/calculation.py b/AmberTools/src/mmpbsa_py/MMPBSA_mods/calculation.py
+index dd010e7..6a2cd98 100644
+--- a/AmberTools/src/mmpbsa_py/MMPBSA_mods/calculation.py
++++ b/AmberTools/src/mmpbsa_py/MMPBSA_mods/calculation.py
+@@ -104,7 +104,8 @@ def run_calculations(FILES, INPUT, rank, MMPBSA_Timer, extern_progs, prefix,
+ 
+       if not stability:
+          # Don't re-run the receptor if we don't have to
+-         if mutant and FILES.receptor_prmtop == FILES.mutant_receptor_prmtop:
++         if mutant and FILES.receptor_prmtop == FILES.mutant_receptor_prmtop \
++                   and not INPUT['mutant_only']:
+             print '  no mutation found in receptor -- using unmutated files'
+             shutil.copy('%sreceptor_gb.mdout.%d' % (
+                         prefix[:prefix.index('mutant')], rank), 
+@@ -127,7 +128,8 @@ def run_calculations(FILES, INPUT, rank, MMPBSA_Timer, extern_progs, prefix,
+             calc.Setup()
+             calc.Run()
+ 
+-         if mutant and FILES.ligand_prmtop == FILES.mutant_ligand_prmtop:
++         if mutant and FILES.ligand_prmtop == FILES.mutant_ligand_prmtop \
++                   and not INPUT['mutant_only']:
+             print '  no mutation found in ligand -- using unmutated files'
+             shutil.copy('%sligand_gb.mdout.%d' % (
+                         prefix[:prefix.index('mutant')], rank), 
+@@ -166,15 +168,16 @@ def run_calculations(FILES, INPUT, rank, MMPBSA_Timer, extern_progs, prefix,
+ 
+       print '  calculating complex contribution...'
+ 
+-      calc = EnergyCalculation(progs['pb'], parmsystem.complex_prmtop,
++      calc = PBEnergyCalculation(progs['pb'], parmsystem.complex_prmtop,
+                    incrd, '%scomplex.%s.%d' % (prefix, trj_sfx, rank), mdin, 
+                    '%scomplex_pb.mdout.%d' % (prefix, rank), 
+                    '_MMPBSA_restrt.%d' % rank)
+       calc.Setup()
+-      calc.Run(stdout=os.devnull)
++      calc.Run()
+ 
+       if not stability:
+-         if mutant and FILES.receptor_prmtop == FILES.mutant_receptor_prmtop:
++         if mutant and FILES.receptor_prmtop == FILES.mutant_receptor_prmtop \
++                   and not INPUT['mutant_only']:
+             print '  no mutation found in receptor -- using unmutated files'
+             shutil.copy('%sreceptor_pb.mdout.%d' % (
+                         prefix[:prefix.index('mutant')], rank), 
+@@ -188,14 +191,15 @@ def run_calculations(FILES, INPUT, rank, MMPBSA_Timer, extern_progs, prefix,
+             if 'mmpbsa_py_energy' in progs['pb']: incrd = '%sreceptor.pdb' % prefix
+             else: incrd = '%sdummyreceptor.inpcrd' % prefix
+    
+-            calc = EnergyCalculation(progs['pb'], parmsystem.receptor_prmtop,
++            calc = PBEnergyCalculation(progs['pb'], parmsystem.receptor_prmtop,
+                      incrd, '%sreceptor.%s.%d' % (prefix, trj_sfx, rank), mdin,
+                      '%sreceptor_pb.mdout.%d' % (prefix, rank),
+                      '_MMPBSA_restrt.%d' % rank)
+             calc.Setup()
+-            calc.Run(stdout=os.devnull)
++            calc.Run()
+ 
+-         if mutant and FILES.ligand_prmtop == FILES.mutant_ligand_prmtop:
++         if mutant and FILES.ligand_prmtop == FILES.mutant_ligand_prmtop \
++                   and not INPUT['mutant_only']:
+             print '  no mutation found in ligand -- using unmutated files'
+             shutil.copy('%sligand_pb.mdout.%d' % (
+                         prefix[:prefix.index('mutant')], rank), 
+@@ -207,12 +211,12 @@ def run_calculations(FILES, INPUT, rank, MMPBSA_Timer, extern_progs, prefix,
+             if 'mmpbsa_py_energy' in progs['pb']: incrd = '%sligand.pdb' % prefix
+             else: incrd = '%sdummyligand.inpcrd' % prefix
+    
+-            calc = EnergyCalculation(progs['pb'], parmsystem.ligand_prmtop,
++            calc = PBEnergyCalculation(progs['pb'], parmsystem.ligand_prmtop,
+                      incrd, '%sligand.%s.%d' % (prefix, trj_sfx, rank), mdin,
+                      '%sligand_pb.mdout.%d' % (prefix, rank),
+                      '_MMPBSA_restrt.%d' % rank)
+             calc.Setup()
+-            calc.Run(stdout=os.devnull)
++            calc.Run()
+ 
+       MMPBSA_Timer.StopTimer('pb')
+ 
+@@ -232,7 +236,8 @@ def run_calculations(FILES, INPUT, rank, MMPBSA_Timer, extern_progs, prefix,
+       calc.Run()
+ 
+       if not stability:
+-         if mutant and FILES.receptor_prmtop == FILES.mutant_receptor_prmtop:
++         if mutant and FILES.receptor_prmtop == FILES.mutant_receptor_prmtop \
++                   and not INPUT['mutant_only']:
+             print '  no mutation found in receptor -- using unmutated files'
+             shutil.copy('%sreceptor_rism.mdout.%d' % (
+                         prefix[:prefix.index('mutant')], rank), 
+@@ -246,7 +251,8 @@ def run_calculations(FILES, INPUT, rank, MMPBSA_Timer, extern_progs, prefix,
+             calc.Setup()
+             calc.Run()
+                
+-         if mutant and FILES.ligand_prmtop == FILES.mutant_ligand_prmtop:
++         if mutant and FILES.ligand_prmtop == FILES.mutant_ligand_prmtop \
++                   and not INPUT['mutant_only']:
+             print '  no mutation found in ligand -- using unmutated files'
+             shutil.copy('%sligand_rism.mdout.%d' % (
+                         prefix[:prefix.index('mutant')], rank), 
+@@ -278,7 +284,8 @@ def run_calculations(FILES, INPUT, rank, MMPBSA_Timer, extern_progs, prefix,
+       calc.Run()
+ 
+       if not stability:
+-         if mutant and FILES.receptor_prmtop == FILES.mutant_receptor_prmtop:
++         if mutant and FILES.receptor_prmtop == FILES.mutant_receptor_prmtop \
++                   and not INPUT['mutant_only']:
+             print '  no mutation found in receptor -- using unmutated files'
+             shutil.copy('%sreceptor_nm.out.%d' % (
+                         prefix[:prefix.index('mutant')], rank), 
+@@ -291,7 +298,8 @@ def run_calculations(FILES, INPUT, rank, MMPBSA_Timer, extern_progs, prefix,
+             calc.Setup()
+             calc.Run()
+ 
+-         if mutant and FILES.ligand_prmtop == FILES.mutant_ligand_prmtop:
++         if mutant and FILES.ligand_prmtop == FILES.mutant_ligand_prmtop \
++                   and not INPUT['mutant_only']:
+             print '  no mutation found in ligand -- using unmutated files'
+             shutil.copy('%sligand_nm.out.%d' % (
+                         prefix[:prefix.index('mutant')], rank), 
+@@ -605,3 +613,55 @@ class QuasiHarmCalc(Calculation):
+       Calculation.Run(self, stdout=self.output)
+ 
+ #+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
++
++class PBEnergyCalculation(EnergyCalculation):
++   """
++   Specially handle the PB calculations to extract warnings and errors PBSA
++   prints to stdout and redirect them to the user
++   """
++   def Run(self, stderr=sys.stderr):
++      """ Runs the program. All command-line arguments must be set before 
++          calling this method. Command-line arguments should be set in Setup()
++      """
++      import re
++      from subprocess import Popen, PIPE
++
++      # If this has not been set up yet
++      # then raise a stink
++      if not self.calc_setup:
++         raise CalcError('Cannot run a calculation without calling its' +
++                        ' its Setup() function!') 
++
++      errorre = re.compile('(pb (?:bomb)|(?:warning))', re.I)
++      # Here, make sure that we could pass a file *OR* a string as stderr.
++      if type(stderr).__name__ == 'str':
++         stderr_is_string = True
++         process_stderr = open(stderr, 'w', 0)
++      else:
++         stderr_is_string = False
++         process_stderr = stderr
++
++      # The Setup() method sets the command-line arguments and makes sure that
++      # all of the CL arguments are set. Now all we have to do is start the 
++      # process and monitor it for success.
++
++      # Popen can only take strings as command-line arguments, so convert 
++      # everything to a string here
++      for i in range(len(self.command_args)):
++         self.command_args[i] = str(self.command_args[i])
++
++      process = Popen(self.command_args, stdin=None, stdout=PIPE,
++                      stderr=process_stderr)
++
++      out, err = process.communicate('')
++      calc_failed = bool(process.wait())
++
++      if stderr_is_string: process_stderr.close()
++
++      if calc_failed:
++         error_list = [s.strip() for s in out.split('\n') 
++                                       if errorre.match(s.strip())]
++         raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
++                         self.prmtop) + '\n\t'.join(error_list) + '\n')
++
++#+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
+diff --git a/AmberTools/src/parmed/ParmedTools/ParmedActions.py b/AmberTools/src/parmed/ParmedTools/ParmedActions.py
+index 4dd905f..4ea4a52 100644
+--- a/AmberTools/src/parmed/ParmedTools/ParmedActions.py
++++ b/AmberTools/src/parmed/ParmedTools/ParmedActions.py
+@@ -604,16 +604,15 @@ class changeljsingletype(Action):
+       from math import sqrt
+       from ParmedTools.exceptions import LJ_TypeError
+       # If this is an empty mask do nothing
+-      if not self.orig_radius: return
++      if self.orig_radius is None: return
+       # Make sure we've only selected a single atom type with our mask
+       attype = None
+-      iter = 0
+-      for sel in self.mask.Selection():
++      for i, sel in enumerate(self.mask.Selection()):
+          if sel == 1:
+-            if not attype:
+-               attype = self.parm.parm_data['ATOM_TYPE_INDEX'][iter]
++            if attype is None:
++               attype = self.parm.parm_data['ATOM_TYPE_INDEX'][i]
+             else:
+-               if attype != self.parm.parm_data['ATOM_TYPE_INDEX'][iter]:
++               if attype != self.parm.parm_data['ATOM_TYPE_INDEX'][i]:
+                   raise LJ_TypeError('changeLJSingleType: ' +
+                           'Selection mask has multiple atom types!')
+       # Fill the Lennard-Jones radius and depth arrays to make sure they're
+@@ -631,10 +630,6 @@ class changeljsingletype(Action):
+          bcoef = 2 * wij * rij ** 6
+          self.parm.parm_data['LENNARD_JONES_ACOEF'][lj_index] = acoef
+          self.parm.parm_data['LENNARD_JONES_BCOEF'][lj_index] = bcoef
+-         lj_index = self.parm.parm_data['NONBONDED_PARM_INDEX'][
+-            self.parm.ptr('ntypes') * (attype-1) + i] - 1
+-         self.parm.parm_data['LENNARD_JONES_ACOEF'][lj_index] = acoef
+-         self.parm.parm_data['LENNARD_JONES_BCOEF'][lj_index] = bcoef
+ 
+ #+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
+ 
+diff --git a/AmberTools/src/pbsa/gen_dx_file.F90 b/AmberTools/src/pbsa/gen_dx_file.F90
+index 475b6ef..d50e453 100644
+--- a/AmberTools/src/pbsa/gen_dx_file.F90
++++ b/AmberTools/src/pbsa/gen_dx_file.F90
+@@ -37,6 +37,7 @@ subroutine gen_dx_file(xm,ym,zm,h,gox,goy,goz,voldata,filename,fn,dataname)
+                         end if
+                     end do
+                 end do; end do
++                if (.not.(MOD(cnt,3).eq. 0) ) write(fn,*) ''
+                 write(fn,*) 'attribute "dep" string "positions"'
+                 write(fn,*) 'object "',dataname,'" class field'
+                 write(fn,*) 'component "positions" value 1'
+diff --git a/AmberTools/src/pbsa/pb_force.F90 b/AmberTools/src/pbsa/pb_force.F90
+index 37337bd..52f1edf 100644
+--- a/AmberTools/src/pbsa/pb_force.F90
++++ b/AmberTools/src/pbsa/pb_force.F90
+@@ -1399,7 +1399,7 @@ subroutine pb_fdfrc( pbverbose,pbprint,pbgrid,ifcap,ipb,imin,natom,atmlast,npdec
+                close(64)
+             elseif ( phiform == 2 ) then
+             !write dx format phi
+-               call gen_dx_file(xm,ym,zm,h,gox,goy,goz,phi(1:xmymzm),&
++               call gen_dx_file(xm,ym,zm,h,gox,goy,goz,frcfac*phi(1:xmymzm),&
+                            phifilename,phifilenum,phidataname)
+ !                write(6,*) 'writing potential map in dx format'
+ !                open(67,file='pbsa_phi.dx')
+diff --git a/AmberTools/src/sqm/constants.F90 b/AmberTools/src/sqm/constants.F90
+index 590cc71..c19fd06 100644
+--- a/AmberTools/src/sqm/constants.F90
++++ b/AmberTools/src/sqm/constants.F90
+@@ -84,18 +84,23 @@ module constants
+   !------------------------------------------------------------
+   !     THE ARRAY FC(I) CONTAINS THE FACTORIALS OF (I-1).
+ 
+-  _REAL_, parameter :: FC(1:17) =&
+-       (/ 1.0D0,1.0D0, 2.0D0, 6.0D0, 24.0D0, 120.0D0, 720.0D0, 5040.0D0, &
+-          40320.0D0, 362880.0D0, 3628800.0D0, 39916800.0D0,              &
+-          4.790016D+08, 6.2270208D+09, 8.71782912D+10,                   &
+-          1.307674368D+12, 2.092278989D+13 /)   
++  _REAL_, parameter :: FC(1:25) =&
++       (/ 1.0D0,1.0D0, 2.0D0, 6.0D0, 24.0D0, &
++          120.0D0, 720.0D0, 5040.0D0, 40320.0D0, 362880.0D0, &
++          3628800.0D0, 39916800.0D0, 4.790016D+08, 6.2270208D+09, 8.71782912D+10, &
++          1.307674368D+12, 2.092278989D+13, 3.55687428096D+14, 6.402373705728D+15, 1.21645100408832D+17, &
++          2.43290200817664D+18, 5.109094217170944D+19, 1.12400072777760768D+21, 2.585201673888497664D+22, &
++                  6.2044840173323943936D+23 /)
+   
+-  _REAL_, parameter :: logFC(1:17) = (/ 0.0D0, 0.0D0, 0.6931471805599D0,       &
++  _REAL_, parameter :: logFC(1:25) = (/ 0.0D0, 0.0D0, 0.6931471805599D0,       &
+        &            1.7917594692281D0,  3.1780538303479D0,  4.7874917427820D0, &
+        &            6.5792512120101D0,  8.5251613610654D0, 10.6046029027453D0, &
+        &           12.8018274800815D0, 15.1044125730755D0, 17.5023078458739D0, &
+        &           19.9872144956619D0, 22.5521638531234D0, 25.1912211827387D0, &
+-       &           27.8992713838409D0, 30.6718601061763D0 /)
++       &           27.8992713838409D0, 30.6718601061763D0, 33.5050734501369D0, &
++                   36.3954452080331D0, 39.3398841871995D0, 42.3356164607535D0, &
++                   45.3801388984769D0, 48.4711813518352D0, 51.6066755677644D0, &
++                   54.7847293981123D0 /)
+ 
+   !     DEFINE C COEFFICIENTS FOR ASSOCIATE LEGENDRE POLYNOMIALS.         
+   _REAL_, parameter::CC(1:21,1:3) = reshape ( (/   &      
+diff --git a/AmberTools/src/sqm/depend b/AmberTools/src/sqm/depend
+index 357ef59..0d3db38 100644
+--- a/AmberTools/src/sqm/depend
++++ b/AmberTools/src/sqm/depend
+@@ -599,7 +599,8 @@ qm2_h1elec_d.o: \
+                     rotation.o\
+                     elementOrbitalIndex.o\
+                     slater_overlap.o\
+-                    qmmm_module.o
++                    qmmm_module.o\
++                    utilitiesModule.o
+ 
+ 
+ qm2_h1elec_d.o:   qm2_h1elec_d.F90
+@@ -668,7 +669,8 @@ qm2_parameters.o: \
+                     elementOrbitalIndex.o\
+                     qmmm_qmtheorymodule.o\
+                     parameterReader.o\
+-                    qmmm_module.o
++                    qmmm_module.o\
++                    utilitiesModule.o
+ 
+ 
+ qm2_parameters.o:   qm2_parameters.F90
+@@ -679,7 +681,8 @@ qm2_params_module.o: \
+                     ../include/assert.fh\
+                     ../include/dprec.fh\
+                     elementOrbitalIndex.o\
+-                    qmmm_qmtheorymodule.o
++                    qmmm_qmtheorymodule.o\
++                    constants.o
+ 
+ 
+ qm2_params_module.o:   qm2_params_module.F90
+diff --git a/AmberTools/src/sqm/qm2_parameters.F90 b/AmberTools/src/sqm/qm2_parameters.F90
+index 9985f1f..e762063 100644
+--- a/AmberTools/src/sqm/qm2_parameters.F90
++++ b/AmberTools/src/sqm/qm2_parameters.F90
+@@ -263,6 +263,8 @@ if (currentTheory%MNDOD) then
+   core_chg( 15) = 5; natomic_orbs( 15) = 9; heat_of_form( 15) = 75.570D0 !P 
+   core_chg( 16) = 6; natomic_orbs( 16) = 9; heat_of_form( 16) = 66.400D0 !S
+   core_chg( 17) = 7; natomic_orbs( 17) = 9; heat_of_form( 17) = 28.990D0 !Cl  
++  core_chg( 35) = 7; natomic_orbs( 35) = 9; heat_of_form( 35) = 26.740D0 !Br
++  core_chg( 53) = 7; natomic_orbs( 53) = 9; heat_of_form( 53) = 25.517D0 !I
+ end if
+ 
+ if (currentTheory%AM1D) then 
+diff --git a/AmberTools/test/mmpbsa_py/04_Per_Residue_Decomp/FINAL_RESULTS_MMPBSA.dat.save b/AmberTools/test/mmpbsa_py/04_Per_Residue_Decomp/FINAL_RESULTS_MMPBSA.dat.save
+index 0390673..f9c1daf 100644
+--- a/AmberTools/test/mmpbsa_py/04_Per_Residue_Decomp/FINAL_RESULTS_MMPBSA.dat.save
++++ b/AmberTools/test/mmpbsa_py/04_Per_Residue_Decomp/FINAL_RESULTS_MMPBSA.dat.save
+@@ -1,11 +1,11 @@
+-| Run on Fri Oct 21 16:59:53 2011
++| Run on Thu Aug 23 19:08:46 2012
+ |
+ |Input file:
+ |--------------------------------------------------------------
+ |MMPBSA input file for running per-residue decomp
+ |&general
+ |   startframe=1, endframe=2, interval=1,
+-|   keep_files=2, debug_printlevel=2
++|   keep_files=1, debug_printlevel=2
+ |/
+ |&gb
+ |   igb=5, saltcon=0.1
+@@ -14,7 +14,7 @@
+ |   idecomp=1, print_res='1-10; 200-241', csv_format=0,
+ |/
+ |--------------------------------------------------------------
+-|MMPBSA.py Version=3.0
++|MMPBSA.py Version=12.0
+ |Solvated complex topology file:  ../EstRAL_Files/sol.top
+ |Complex topology file:           ../EstRAL_Files/com.top
+ |Receptor topology file:          ../EstRAL_Files/rec.top
+@@ -38,13 +38,13 @@ Energy Component            Average              Std. Dev.   Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS                  -2027.4585                6.6828              4.7254
+ EEL                     -17102.0128               39.7611             28.1154
+-EGB                      -3036.0661               15.1517             10.7138
+-ESURF                       92.0643                0.2456              0.1737
++EGB                      -3036.2753               15.1544             10.7158
++ESURF                       92.0404                0.2552              0.1805
+ 
+ G gas                   -19129.4713               46.4439             32.8408
+-G solv                   -2944.0018               15.3973             10.8875
++G solv                   -2944.2348               15.4096             10.8963
+ 
+-TOTAL                   -22073.4731               31.0467             21.9533
++TOTAL                   -22073.7061               31.0343             21.9445
+ 
+ 
+ Receptor:
+@@ -52,13 +52,13 @@ Energy Component            Average              Std. Dev.   Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS                  -1963.0469                6.3796              4.5110
+ EEL                     -17062.3941               41.4017             29.2755
+-EGB                      -3045.5263               17.9328             12.6804
+-ESURF                       94.5901                0.3006              0.2125
++EGB                      -3045.7452               17.9344             12.6815
++ESURF                       94.5395                0.3071              0.2171
+ 
+ G gas                   -19025.4410               47.7813             33.7865
+-G solv                   -2950.9362               18.2334             12.8929
++G solv                   -2951.2056               18.2415             12.8987
+ 
+-TOTAL                   -21976.3773               29.5480             20.8936
++TOTAL                   -21976.6467               29.5398             20.8878
+ 
+ 
+ Ligand:
+@@ -66,13 +66,13 @@ Energy Component            Average              Std. Dev.   Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS                     -2.1842                0.9276              0.6559
+ EEL                         -5.8905                0.2643              0.1869
+-EGB                        -28.9823                0.3972              0.2809
+-ESURF                        5.5752                0.0080              0.0057
++EGB                        -28.9847                0.3972              0.2809
++ESURF                        5.5941                0.0255              0.0181
+ 
+ G gas                       -8.0747                1.1919              0.8428
+-G solv                     -23.4071                0.4052              0.2865
++G solv                     -23.3905                0.4228              0.2989
+ 
+-TOTAL                      -31.4819                1.5971              1.1293
++TOTAL                      -31.4653                1.6146              1.1417
+ 
+ 
+ Differences (Complex - Receptor - Ligand):
+@@ -80,13 +80,13 @@ Energy Component            Average              Std. Dev.   Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS                    -62.2274                1.2308              0.8703
+ EEL                        -33.7281                1.3763              0.9732
+-EGB                         38.4425                3.1784              2.2474
+-ESURF                       -8.1010                0.0630              0.0445
++EGB                         38.4546                3.1772              2.2466
++ESURF                       -8.0932                0.0774              0.0547
+ 
+ DELTA G gas                -95.9555                0.1455              0.1029
+-DELTA G solv                30.3415                3.2413              2.2919
++DELTA G solv                30.3614                3.2545              2.3013
+ 
+-DELTA TOTAL                -65.6140                3.0958              2.1890
++DELTA TOTAL                -65.5942                3.1090              2.1984
+ 
+ 
+ -------------------------------------------------------------------------------
+diff --git a/AmberTools/test/mmpbsa_py/05_Pairwise_Decomp/FINAL_RESULTS_MMPBSA.dat.save b/AmberTools/test/mmpbsa_py/05_Pairwise_Decomp/FINAL_RESULTS_MMPBSA.dat.save
+index f7cbe88..2135ffe 100644
+--- a/AmberTools/test/mmpbsa_py/05_Pairwise_Decomp/FINAL_RESULTS_MMPBSA.dat.save
++++ b/AmberTools/test/mmpbsa_py/05_Pairwise_Decomp/FINAL_RESULTS_MMPBSA.dat.save
+@@ -1,11 +1,11 @@
+-| Run on Fri Oct 21 17:35:19 2011
++| Run on Thu Aug 23 19:09:35 2012
+ |
+ |Input file:
+ |--------------------------------------------------------------
+ |MMPBSA input file for running per-residue decomp
+ |&general
+ |   startframe=1, endframe=2, interval=1,
+-|   keep_files=2, debug_printlevel=2,
++|   keep_files=0, debug_printlevel=2,
+ |/
+ |&gb
+ |   igb=5, saltcon=0.1
+@@ -15,7 +15,7 @@
+ |   csv_format=0,
+ |/
+ |--------------------------------------------------------------
+-|MMPBSA.py Version=3.0
++|MMPBSA.py Version=12.0
+ |Solvated complex topology file:  ../EstRAL_Files/sol.top
+ |Complex topology file:           ../EstRAL_Files/com.top
+ |Receptor topology file:          ../EstRAL_Files/rec.top
+@@ -39,13 +39,13 @@ Energy Component            Average              Std. Dev.   Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS                  -2027.4585                6.6828              4.7254
+ EEL                     -17102.0128               39.7611             28.1154
+-EGB                      -3036.0661               15.1517             10.7138
+-ESURF                       92.0643                0.2456              0.1737
++EGB                      -3036.2753               15.1544             10.7158
++ESURF                       92.0404                0.2552              0.1805
+ 
+ G gas                   -19129.4713               46.4439             32.8408
+-G solv                   -2944.0018               15.3973             10.8875
++G solv                   -2944.2348               15.4096             10.8963
+ 
+-TOTAL                   -22073.4731               31.0467             21.9533
++TOTAL                   -22073.7061               31.0343             21.9445
+ 
+ 
+ Receptor:
+@@ -53,13 +53,13 @@ Energy Component            Average              Std. Dev.   Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS                  -1963.0469                6.3796              4.5110
+ EEL                     -17062.3941               41.4017             29.2755
+-EGB                      -3045.5263               17.9328             12.6804
+-ESURF                       94.5901                0.3006              0.2125
++EGB                      -3045.7452               17.9344             12.6815
++ESURF                       94.5395                0.3071              0.2171
+ 
+ G gas                   -19025.4410               47.7813             33.7865
+-G solv                   -2950.9362               18.2334             12.8929
++G solv                   -2951.2056               18.2415             12.8987
+ 
+-TOTAL                   -21976.3773               29.5480             20.8936
++TOTAL                   -21976.6467               29.5398             20.8878
+ 
+ 
+ Ligand:
+@@ -67,13 +67,13 @@ Energy Component            Average              Std. Dev.   Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS                     -2.1842                0.9276              0.6559
+ EEL                         -5.8905                0.2643              0.1869
+-EGB                        -28.9823                0.3972              0.2809
+-ESURF                        5.5752                0.0080              0.0057
++EGB                        -28.9847                0.3972              0.2809
++ESURF                        5.5941                0.0255              0.0181
+ 
+ G gas                       -8.0747                1.1919              0.8428
+-G solv                     -23.4071                0.4052              0.2865
++G solv                     -23.3905                0.4228              0.2989
+ 
+-TOTAL                      -31.4819                1.5971              1.1293
++TOTAL                      -31.4653                1.6146              1.1417
+ 
+ 
+ Differences (Complex - Receptor - Ligand):
+@@ -81,13 +81,13 @@ Energy Component            Average              Std. Dev.   Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS                    -62.2274                1.2308              0.8703
+ EEL                        -33.7281                1.3763              0.9732
+-EGB                         38.4425                3.1784              2.2474
+-ESURF                       -8.1010                0.0630              0.0445
++EGB                         38.4546                3.1772              2.2466
++ESURF                       -8.0932                0.0774              0.0547
+ 
+ DELTA G gas                -95.9555                0.1455              0.1029
+-DELTA G solv                30.3415                3.2413              2.2919
++DELTA G solv                30.3614                3.2545              2.3013
+ 
+-DELTA TOTAL                -65.6140                3.0958              2.1890
++DELTA TOTAL                -65.5942                3.1090              2.1984
+ 
+ 
+ -------------------------------------------------------------------------------
+diff --git a/AmberTools/test/mmpbsa_py/10_QM_MMGBSA/FINAL_RESULTS_MMPBSA.dat.save b/AmberTools/test/mmpbsa_py/10_QM_MMGBSA/FINAL_RESULTS_MMPBSA.dat.save
+index 1c6672d..4dc52b5 100644
+--- a/AmberTools/test/mmpbsa_py/10_QM_MMGBSA/FINAL_RESULTS_MMPBSA.dat.save
++++ b/AmberTools/test/mmpbsa_py/10_QM_MMGBSA/FINAL_RESULTS_MMPBSA.dat.save
+@@ -1,4 +1,4 @@
+-| Run on Sun Feb 19 11:48:15 2012
++| Run on Thu Aug 23 19:12:17 2012
+ |
+ |Input file:
+ |--------------------------------------------------------------
+@@ -13,7 +13,7 @@
+ |   qm_theory='PM3',
+ |/
+ |--------------------------------------------------------------
+-|MMPBSA.py Version=3.1
++|MMPBSA.py Version=12.0
+ |Solvated complex topology file:  ../EstRAL_Files/sol.top
+ |Complex topology file:           ../EstRAL_Files/com.top
+ |Receptor topology file:          ../EstRAL_Files/rec.top
+@@ -38,14 +38,14 @@ Energy Component            Average              Std. Dev.   Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS                  -2025.2744                7.6103              5.3813
+ EEL                     -17062.4395               41.4020             29.2756
+-EGB                      -3038.1307               14.7141             10.4045
++EGB                      -3038.3396               14.7163             10.4060
+ ESURF                       96.5366                0.2385              0.1686
+-ESCF                       -21.6928                3.7699              2.6658
++ESCF                       -21.6939                3.7699              2.6657
+ 
+ G gas                   -19087.7139               49.0123             34.6570
+-G solv                   -2941.5940               14.4757             10.2358
++G solv                   -2941.8030               14.4778             10.2374
+ 
+-TOTAL                   -22051.0007               30.7667             21.7554
++TOTAL                   -22051.2107               30.7647             21.7539
+ 
+ 
+ Receptor:
+@@ -53,26 +53,26 @@ Energy Component            Average              Std. Dev.   Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS                  -1963.0469                6.3796              4.5110
+ EEL                     -17062.3941               41.4017             29.2755
+-EGB                      -3045.5263               17.9328             12.6804
++EGB                      -3045.7452               17.9344             12.6815
+ ESURF                      100.5546                0.3074              0.2173
+ 
+ G gas                   -19025.4410               47.7813             33.7865
+-G solv                   -2944.9718               17.6255             12.4631
++G solv                   -2945.1907               17.6270             12.4642
+ 
+-TOTAL                   -21970.4127               30.1558             21.3234
++TOTAL                   -21970.6316               30.1543             21.3223
+ 
+ 
+ Ligand:
+ Energy Component            Average              Std. Dev.   Std. Err. of Mean
+ -------------------------------------------------------------------------------
+-EGB                        -24.0340                0.8659              0.6123
++EGB                        -24.0371                0.8661              0.6124
+ ESURF                        4.4275                0.0229              0.0162
+-ESCF                         6.8997                1.2609              0.8916
++ESCF                         6.9011                1.2609              0.8916
+ 
+ G gas                        0.0000                0.0000              0.0000
+-G solv                     -19.6065                0.8889              0.6285
++G solv                     -19.6096                0.8891              0.6287
+ 
+-TOTAL                      -12.7069                2.1498              1.5201
++TOTAL                      -12.7085                2.1499              1.5202
+ 
+ 
+ Differences (Complex - Receptor - Ligand):
+@@ -80,14 +80,14 @@ Energy Component            Average              Std. Dev.   Std. Err. of Mean
+ -------------------------------------------------------------------------------
+ VDWAALS                    -62.2274                1.2308              0.8703
+ EEL                         -0.0454                0.0003              0.0002
+-EGB                         31.4297                4.0846              2.8882
++EGB                         31.4427                4.0842              2.8880
+ ESURF                       -8.4454                0.0459              0.0325
+-ESCF                       -28.5925                2.5090              1.7741
++ESCF                       -28.5950                2.5090              1.7741
+ 
+ DELTA G gas                -62.2728                1.2310              0.8705
+-DELTA G solv                22.9843                4.0386              2.8558
++DELTA G solv                22.9973                4.0383              2.8555
+ 
+-DELTA TOTAL                -67.8811                2.7607              1.9521
++DELTA TOTAL                -67.8705                2.7603              1.9519
+ 
+ 
+ -------------------------------------------------------------------------------
+diff --git a/AmberTools/test/parmed/normal_prmtop/final.prmtop.save b/AmberTools/test/parmed/normal_prmtop/final.prmtop.save
+index a7e4428..3ce70b7 100644
+--- a/AmberTools/test/parmed/normal_prmtop/final.prmtop.save
++++ b/AmberTools/test/parmed/normal_prmtop/final.prmtop.save
+@@ -1,4 +1,4 @@
+-%VERSION  VERSION_STAMP = V0001.000  DATE = 02/28/12  13:10:17
++%VERSION  VERSION_STAMP = V0001.000  DATE = 07/08/12  15:11:06
+ %FLAG TITLE
+ %FORMAT(20a4)
+ 
+@@ -1245,63 +1245,63 @@ GLU PHE LEU ASP ALA ASN LEU ALA
+   0.00000000E+00  0.00000000E+00
+ %FLAG LENNARD_JONES_ACOEF
+ %FORMAT(5E16.8)
+-  9.44293233E+05  2.12601181E+03  1.39982777E-01  9.95480466E+05  2.56678134E+03
+-  1.04308023E+06  2.01791425E+04  9.14716912E+00  2.27401052E+04  2.01823541E+02
+-  6.20665997E+04  5.94667300E+01  6.78771368E+04  8.79040886E+02  3.25969625E+03
+-  7.44975864E+05  1.40467023E+03  7.91544157E+05  1.45985502E+04  4.66922514E+04
++  9.44293233E+05  2.12601181E+03  1.39982777E-01  9.96389997E+05  2.56912650E+03
++  1.04498714E+06  2.01791425E+04  9.14716912E+00  2.27608820E+04  2.01823541E+02
++  6.20665997E+04  5.94667300E+01  6.79391534E+04  8.79040886E+02  3.25969625E+03
++  7.44975864E+05  1.40467023E+03  7.92267358E+05  1.45985502E+04  4.66922514E+04
+   5.81803229E+05  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+   0.00000000E+00  0.00000000E+00  0.00000000E+00  8.82619071E+05  2.27577561E+03
+-  9.24822270E+05  2.01619733E+04  6.01816484E+04  7.01803794E+05  0.00000000E+00
+-  8.19971662E+05  6.06829342E+05  1.02595236E+03  6.47841731E+05  1.12780457E+04
++  9.25667242E+05  2.01619733E+04  6.01816484E+04  7.01803794E+05  0.00000000E+00
++  8.19971662E+05  6.06829342E+05  1.02595236E+03  6.48433639E+05  1.12780457E+04
+   3.69471530E+04  4.71003287E+05  0.00000000E+00  5.74393458E+05  3.79876399E+05
+-  8.96776989E+04  1.07193646E+02  9.71708117E+04  1.41077189E+03  4.98586848E+03
++  8.96776989E+04  1.07193646E+02  9.72595927E+04  1.41077189E+03  4.98586848E+03
+   6.82786631E+04  0.00000000E+00  8.61541883E+04  5.44261042E+04  7.51607703E+03
+-  5.46147253E+04  4.90239937E+01  5.98885646E+04  7.50063100E+02  2.82099197E+03
++  5.46147253E+04  4.90239937E+01  5.99432824E+04  7.50063100E+02  2.82099197E+03
+   4.09427581E+04  0.00000000E+00  5.30987710E+04  3.23283631E+04  4.33325458E+03
+-  2.43828624E+03  6.58473870E+04  6.63368273E+01  7.18621074E+04  9.55000044E+02
++  2.43828624E+03  6.58473870E+04  6.63368273E+01  7.19277648E+04  9.55000044E+02
+   3.50301067E+03  4.96707306E+04  0.00000000E+00  6.37148278E+04  3.93690817E+04
+   5.34045360E+03  3.03448006E+03  3.76169105E+03  7.91627154E+04  8.90987508E+01
+-  8.59947003E+04  1.21014911E+03  4.33325458E+03  6.00750218E+04  0.00000000E+00
++  8.60732702E+04  1.21014911E+03  4.33325458E+03  6.00750218E+04  0.00000000E+00
+   7.62451550E+04  4.77908183E+04  6.55825601E+03  3.76169105E+03  4.64559155E+03
+-  5.71629601E+03  2.01562190E+06  5.97860700E+03  2.09861767E+06  4.93469320E+04
++  5.71629601E+03  2.01562190E+06  5.97860700E+03  2.10053510E+06  4.93469320E+04
+   1.42791446E+05  1.61587928E+06  0.00000000E+00  1.86068943E+06  1.32911052E+06
+   2.02461849E+05  1.26338489E+05  1.50848032E+05  1.79647996E+05  4.19430400E+06
+-  9.96389997E+05  2.56912650E+03  1.04403325E+06  2.27608820E+04  6.79391534E+04
+-  7.92267358E+05  0.00000000E+00  9.25667242E+05  6.48433639E+05  9.72595927E+04
+-  5.99432824E+04  7.19277648E+04  8.60732702E+04  2.10053510E+06  1.04498714E+06
+-  8.82619071E+05  2.27577560E+03  9.24822269E+05  2.01619733E+04  6.01816484E+04
++  9.44293233E+05  2.12601181E+03  9.96389997E+05  2.01791425E+04  6.20665998E+04
++  7.44975864E+05  0.00000000E+00  8.82619071E+05  6.06829343E+05  8.96776989E+04
++  5.46147253E+04  6.58473870E+04  7.91627155E+04  2.01562190E+06  9.44293233E+05
++  8.82619071E+05  2.27577560E+03  9.25667242E+05  2.01619733E+04  6.01816484E+04
+   7.01803794E+05  0.00000000E+00  8.19971662E+05  5.74393458E+05  8.61541883E+04
+-  5.30987710E+04  6.37148277E+04  7.62451551E+04  1.86068943E+06  9.25667242E+05
++  5.30987710E+04  6.37148277E+04  7.62451551E+04  1.86068943E+06  2.00000000E+00
+   8.19971662E+05
+ %FLAG LENNARD_JONES_BCOEF
+ %FORMAT(5E16.8)
+-  8.01323529E+02  2.09604198E+01  9.37598976E-02  7.36907417E+02  2.06278363E+01
+-  6.75612247E+02  6.45756063E+01  7.57919667E-01  6.13981767E+01  3.56012899E+00
+-  1.13252061E+02  1.93248820E+00  1.06076943E+02  7.42992380E+00  1.43076527E+01
+-  7.50714425E+02  1.79702257E+01  6.93079947E+02  5.79323581E+01  1.03606917E+02
++  8.01323529E+02  2.09604198E+01  9.37598976E-02  7.37580700E+02  2.06466831E+01
++  6.76847370E+02  6.45756063E+01  7.57919667E-01  6.14542738E+01  3.56012899E+00
++  1.13252061E+02  1.93248820E+00  1.06173862E+02  7.42992380E+00  1.43076527E+01
++  7.50714425E+02  1.79702257E+01  6.93713186E+02  5.79323581E+01  1.03606917E+02
+   6.99746810E+02  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+   0.00000000E+00  0.00000000E+00  0.00000000E+00  6.53361429E+02  1.82891803E+01
+-  5.99015525E+02  5.44372326E+01  9.40505980E+01  6.14502845E+02  0.00000000E+00
+-  5.31102864E+02  6.77220874E+02  1.53505284E+01  6.26720080E+02  5.08951803E+01
++  5.99562822E+02  5.44372326E+01  9.40505980E+01  6.14502845E+02  0.00000000E+00
++  5.31102864E+02  6.77220874E+02  1.53505284E+01  6.27292689E+02  5.08951803E+01
+   9.21192136E+01  6.29300710E+02  0.00000000E+00  5.55666448E+02  5.64885984E+02
+-  1.36131731E+02  2.59456373E+00  1.26919150E+02  9.41257003E+00  1.76949863E+01
++  1.36131731E+02  2.59456373E+00  1.27035111E+02  9.41257003E+00  1.76949863E+01
+   1.25287818E+02  0.00000000E+00  1.12529845E+02  1.11805549E+02  2.17257828E+01
+-  1.05031585E+02  1.73473071E+00  9.85097219E+01  6.78541827E+00  1.31591746E+01
++  1.05031585E+02  1.73473071E+00  9.85997263E+01  6.78541827E+00  1.31591746E+01
+   9.59185913E+01  0.00000000E+00  8.73413012E+01  8.51921330E+01  1.63092814E+01
+-  1.20953369E+01  1.15327881E+02  2.01792524E+00  1.07908863E+02  7.65648470E+00
++  1.20953369E+01  1.15327881E+02  2.01792524E+00  1.08007455E+02  7.65648470E+00
+   1.46638650E+01  1.05648788E+02  0.00000000E+00  9.56748258E+01  9.40124296E+01
+   1.81057616E+01  1.34932874E+01  1.50233639E+01  1.26451907E+02  2.33864085E+00
+-  1.18043746E+02  8.61880722E+00  1.63092814E+01  1.16187983E+02  0.00000000E+00
++  1.18151598E+02  8.61880722E+00  1.63092814E+01  1.16187983E+02  0.00000000E+00
+   1.04660679E+02  1.03580945E+02  2.00642027E+01  1.50233639E+01  1.66953734E+01
+-  1.85196588E+01  1.28923404E+03  3.87070358E+01  1.17824605E+03  1.11203892E+02
++  1.85196588E+01  1.28923404E+03  3.87070358E+01  1.17932256E+03  1.11203892E+02
+   1.89165096E+02  1.21753341E+03  0.00000000E+00  1.04466382E+03  1.10369829E+03
+   2.25248294E+02  1.75916126E+02  1.92224012E+02  2.09772716E+02  2.04800000E+03
+-  7.37580700E+02  2.06466831E+01  6.76229527E+02  6.14542738E+01  1.06173862E+02
+-  6.93713186E+02  0.00000000E+00  5.99562822E+02  6.27292689E+02  1.27035111E+02
+-  9.85997263E+01  1.08007455E+02  1.18151598E+02  1.17932256E+03  6.76847370E+02
+-  6.53361429E+02  1.82891803E+01  5.99015525E+02  5.44372327E+01  9.40505981E+01
++  8.01323529E+02  2.09604198E+01  7.37580700E+02  6.45756063E+01  1.13252062E+02
++  7.50714426E+02  0.00000000E+00  6.53361429E+02  6.77220874E+02  1.36131731E+02
++  1.05031585E+02  1.15327881E+02  1.26451907E+02  1.28923404E+03  8.01323529E+02
++  6.53361429E+02  1.82891803E+01  5.99562822E+02  5.44372327E+01  9.40505981E+01
+   6.14502846E+02  0.00000000E+00  5.31102864E+02  5.55666449E+02  1.12529845E+02
+-  8.73413013E+01  9.56748257E+01  1.04660679E+02  1.04466382E+03  5.99562822E+02
++  8.73413013E+01  9.56748257E+01  1.04660679E+02  1.04466382E+03  4.00000000E+00
+   5.31102864E+02
+ %FLAG BONDS_INC_HYDROGEN
+ %FORMAT(10I8)
+diff --git a/AmberTools/test/parmed/normal_prmtop/prmtop.add_AtNum.save b/AmberTools/test/parmed/normal_prmtop/prmtop.add_AtNum.save
+index a7e4428..3ce70b7 100644
+--- a/AmberTools/test/parmed/normal_prmtop/prmtop.add_AtNum.save
++++ b/AmberTools/test/parmed/normal_prmtop/prmtop.add_AtNum.save
+@@ -1,4 +1,4 @@
+-%VERSION  VERSION_STAMP = V0001.000  DATE = 02/28/12  13:10:17
++%VERSION  VERSION_STAMP = V0001.000  DATE = 07/08/12  15:11:06
+ %FLAG TITLE
+ %FORMAT(20a4)
+ 
+@@ -1245,63 +1245,63 @@ GLU PHE LEU ASP ALA ASN LEU ALA
+   0.00000000E+00  0.00000000E+00
+ %FLAG LENNARD_JONES_ACOEF
+ %FORMAT(5E16.8)
+-  9.44293233E+05  2.12601181E+03  1.39982777E-01  9.95480466E+05  2.56678134E+03
+-  1.04308023E+06  2.01791425E+04  9.14716912E+00  2.27401052E+04  2.01823541E+02
+-  6.20665997E+04  5.94667300E+01  6.78771368E+04  8.79040886E+02  3.25969625E+03
+-  7.44975864E+05  1.40467023E+03  7.91544157E+05  1.45985502E+04  4.66922514E+04
++  9.44293233E+05  2.12601181E+03  1.39982777E-01  9.96389997E+05  2.56912650E+03
++  1.04498714E+06  2.01791425E+04  9.14716912E+00  2.27608820E+04  2.01823541E+02
++  6.20665997E+04  5.94667300E+01  6.79391534E+04  8.79040886E+02  3.25969625E+03
++  7.44975864E+05  1.40467023E+03  7.92267358E+05  1.45985502E+04  4.66922514E+04
+   5.81803229E+05  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+   0.00000000E+00  0.00000000E+00  0.00000000E+00  8.82619071E+05  2.27577561E+03
+-  9.24822270E+05  2.01619733E+04  6.01816484E+04  7.01803794E+05  0.00000000E+00
+-  8.19971662E+05  6.06829342E+05  1.02595236E+03  6.47841731E+05  1.12780457E+04
++  9.25667242E+05  2.01619733E+04  6.01816484E+04  7.01803794E+05  0.00000000E+00
++  8.19971662E+05  6.06829342E+05  1.02595236E+03  6.48433639E+05  1.12780457E+04
+   3.69471530E+04  4.71003287E+05  0.00000000E+00  5.74393458E+05  3.79876399E+05
+-  8.96776989E+04  1.07193646E+02  9.71708117E+04  1.41077189E+03  4.98586848E+03
++  8.96776989E+04  1.07193646E+02  9.72595927E+04  1.41077189E+03  4.98586848E+03
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+-  5.46147253E+04  4.90239937E+01  5.98885646E+04  7.50063100E+02  2.82099197E+03
++  5.46147253E+04  4.90239937E+01  5.99432824E+04  7.50063100E+02  2.82099197E+03
+   4.09427581E+04  0.00000000E+00  5.30987710E+04  3.23283631E+04  4.33325458E+03
+-  2.43828624E+03  6.58473870E+04  6.63368273E+01  7.18621074E+04  9.55000044E+02
++  2.43828624E+03  6.58473870E+04  6.63368273E+01  7.19277648E+04  9.55000044E+02
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+   5.34045360E+03  3.03448006E+03  3.76169105E+03  7.91627154E+04  8.90987508E+01
+-  8.59947003E+04  1.21014911E+03  4.33325458E+03  6.00750218E+04  0.00000000E+00
++  8.60732702E+04  1.21014911E+03  4.33325458E+03  6.00750218E+04  0.00000000E+00
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+-  5.71629601E+03  2.01562190E+06  5.97860700E+03  2.09861767E+06  4.93469320E+04
++  5.71629601E+03  2.01562190E+06  5.97860700E+03  2.10053510E+06  4.93469320E+04
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+-  9.96389997E+05  2.56912650E+03  1.04403325E+06  2.27608820E+04  6.79391534E+04
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+-  5.99432824E+04  7.19277648E+04  8.60732702E+04  2.10053510E+06  1.04498714E+06
+-  8.82619071E+05  2.27577560E+03  9.24822269E+05  2.01619733E+04  6.01816484E+04
++  9.44293233E+05  2.12601181E+03  9.96389997E+05  2.01791425E+04  6.20665998E+04
++  7.44975864E+05  0.00000000E+00  8.82619071E+05  6.06829343E+05  8.96776989E+04
++  5.46147253E+04  6.58473870E+04  7.91627155E+04  2.01562190E+06  9.44293233E+05
++  8.82619071E+05  2.27577560E+03  9.25667242E+05  2.01619733E+04  6.01816484E+04
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++  5.30987710E+04  6.37148277E+04  7.62451551E+04  1.86068943E+06  2.00000000E+00
+   8.19971662E+05
+ %FLAG LENNARD_JONES_BCOEF
+ %FORMAT(5E16.8)
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++  5.31102864E+02  6.77220874E+02  1.53505284E+01  6.27292689E+02  5.08951803E+01
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++  1.36131731E+02  2.59456373E+00  1.27035111E+02  9.41257003E+00  1.76949863E+01
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++  1.85196588E+01  1.28923404E+03  3.87070358E+01  1.17932256E+03  1.11203892E+02
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+-  6.93713186E+02  0.00000000E+00  5.99562822E+02  6.27292689E+02  1.27035111E+02
+-  9.85997263E+01  1.08007455E+02  1.18151598E+02  1.17932256E+03  6.76847370E+02
+-  6.53361429E+02  1.82891803E+01  5.99015525E+02  5.44372327E+01  9.40505981E+01
++  8.01323529E+02  2.09604198E+01  7.37580700E+02  6.45756063E+01  1.13252062E+02
++  7.50714426E+02  0.00000000E+00  6.53361429E+02  6.77220874E+02  1.36131731E+02
++  1.05031585E+02  1.15327881E+02  1.26451907E+02  1.28923404E+03  8.01323529E+02
++  6.53361429E+02  1.82891803E+01  5.99562822E+02  5.44372327E+01  9.40505981E+01
+   6.14502846E+02  0.00000000E+00  5.31102864E+02  5.55666449E+02  1.12529845E+02
+-  8.73413013E+01  9.56748257E+01  1.04660679E+02  1.04466382E+03  5.99562822E+02
++  8.73413013E+01  9.56748257E+01  1.04660679E+02  1.04466382E+03  4.00000000E+00
+   5.31102864E+02
+ %FLAG BONDS_INC_HYDROGEN
+ %FORMAT(10I8)
+diff --git a/AmberTools/test/parmed/normal_prmtop/prmtop.new_lj.save b/AmberTools/test/parmed/normal_prmtop/prmtop.new_lj.save
+index 0a2a704..d984445 100644
+--- a/AmberTools/test/parmed/normal_prmtop/prmtop.new_lj.save
++++ b/AmberTools/test/parmed/normal_prmtop/prmtop.new_lj.save
+@@ -1,4 +1,4 @@
+-%VERSION  VERSION_STAMP = V0001.000  DATE = 02/21/12  17:31:04
++%VERSION  VERSION_STAMP = V0001.000  DATE = 07/08/12  15:11:06
+ %FLAG TITLE
+ %FORMAT(20a4)
+ 
+@@ -1245,63 +1245,63 @@ GLU PHE LEU ASP ALA ASN LEU ALA
+   0.00000000E+00  0.00000000E+00
+ %FLAG LENNARD_JONES_ACOEF
+ %FORMAT(5E16.8)
+-  9.44293233E+05  2.12601181E+03  1.39982777E-01  9.95480466E+05  2.56678134E+03
+-  1.04308023E+06  2.01791425E+04  9.14716912E+00  2.27401052E+04  2.01823541E+02
+-  6.20665997E+04  5.94667300E+01  6.78771368E+04  8.79040886E+02  3.25969625E+03
+-  7.44975864E+05  1.40467023E+03  7.91544157E+05  1.45985502E+04  4.66922514E+04
++  9.44293233E+05  2.12601181E+03  1.39982777E-01  9.96389997E+05  2.56912650E+03
++  1.04498714E+06  2.01791425E+04  9.14716912E+00  2.27608820E+04  2.01823541E+02
++  6.20665997E+04  5.94667300E+01  6.79391534E+04  8.79040886E+02  3.25969625E+03
++  7.44975864E+05  1.40467023E+03  7.92267358E+05  1.45985502E+04  4.66922514E+04
+   5.81803229E+05  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+   0.00000000E+00  0.00000000E+00  0.00000000E+00  8.82619071E+05  2.27577561E+03
+-  9.24822270E+05  2.01619733E+04  6.01816484E+04  7.01803794E+05  0.00000000E+00
+-  8.19971662E+05  6.06829342E+05  1.02595236E+03  6.47841731E+05  1.12780457E+04
++  9.25667242E+05  2.01619733E+04  6.01816484E+04  7.01803794E+05  0.00000000E+00
++  8.19971662E+05  6.06829342E+05  1.02595236E+03  6.48433639E+05  1.12780457E+04
+   3.69471530E+04  4.71003287E+05  0.00000000E+00  5.74393458E+05  3.79876399E+05
+-  8.96776989E+04  1.07193646E+02  9.71708117E+04  1.41077189E+03  4.98586848E+03
++  8.96776989E+04  1.07193646E+02  9.72595927E+04  1.41077189E+03  4.98586848E+03
+   6.82786631E+04  0.00000000E+00  8.61541883E+04  5.44261042E+04  7.51607703E+03
+-  5.46147253E+04  4.90239937E+01  5.98885646E+04  7.50063100E+02  2.82099197E+03
++  5.46147253E+04  4.90239937E+01  5.99432824E+04  7.50063100E+02  2.82099197E+03
+   4.09427581E+04  0.00000000E+00  5.30987710E+04  3.23283631E+04  4.33325458E+03
+-  2.43828624E+03  6.58473870E+04  6.63368273E+01  7.18621074E+04  9.55000044E+02
++  2.43828624E+03  6.58473870E+04  6.63368273E+01  7.19277648E+04  9.55000044E+02
+   3.50301067E+03  4.96707306E+04  0.00000000E+00  6.37148278E+04  3.93690817E+04
+   5.34045360E+03  3.03448006E+03  3.76169105E+03  7.91627154E+04  8.90987508E+01
+-  8.59947003E+04  1.21014911E+03  4.33325458E+03  6.00750218E+04  0.00000000E+00
++  8.60732702E+04  1.21014911E+03  4.33325458E+03  6.00750218E+04  0.00000000E+00
+   7.62451550E+04  4.77908183E+04  6.55825601E+03  3.76169105E+03  4.64559155E+03
+-  5.71629601E+03  2.01562190E+06  5.97860700E+03  2.09861767E+06  4.93469320E+04
++  5.71629601E+03  2.01562190E+06  5.97860700E+03  2.10053510E+06  4.93469320E+04
+   1.42791446E+05  1.61587928E+06  0.00000000E+00  1.86068943E+06  1.32911052E+06
+   2.02461849E+05  1.26338489E+05  1.50848032E+05  1.79647996E+05  4.19430400E+06
+-  9.96389997E+05  2.56912650E+03  1.04403325E+06  2.27608820E+04  6.79391534E+04
+-  7.92267358E+05  0.00000000E+00  9.25667242E+05  6.48433639E+05  9.72595927E+04
+-  5.99432824E+04  7.19277648E+04  8.60732702E+04  2.10053510E+06  1.04498714E+06
+-  8.82619071E+05  2.27577560E+03  9.24822269E+05  2.01619733E+04  6.01816484E+04
++  9.44293233E+05  2.12601181E+03  9.96389997E+05  2.01791425E+04  6.20665998E+04
++  7.44975864E+05  0.00000000E+00  8.82619071E+05  6.06829343E+05  8.96776989E+04
++  5.46147253E+04  6.58473870E+04  7.91627155E+04  2.01562190E+06  9.44293233E+05
++  8.82619071E+05  2.27577560E+03  9.25667242E+05  2.01619733E+04  6.01816484E+04
+   7.01803794E+05  0.00000000E+00  8.19971662E+05  5.74393458E+05  8.61541883E+04
+-  5.30987710E+04  6.37148277E+04  7.62451551E+04  1.86068943E+06  9.25667242E+05
++  5.30987710E+04  6.37148277E+04  7.62451551E+04  1.86068943E+06  2.00000000E+00
+   8.19971662E+05
+ %FLAG LENNARD_JONES_BCOEF
+ %FORMAT(5E16.8)
+-  8.01323529E+02  2.09604198E+01  9.37598976E-02  7.36907417E+02  2.06278363E+01
+-  6.75612247E+02  6.45756063E+01  7.57919667E-01  6.13981767E+01  3.56012899E+00
+-  1.13252061E+02  1.93248820E+00  1.06076943E+02  7.42992380E+00  1.43076527E+01
+-  7.50714425E+02  1.79702257E+01  6.93079947E+02  5.79323581E+01  1.03606917E+02
++  8.01323529E+02  2.09604198E+01  9.37598976E-02  7.37580700E+02  2.06466831E+01
++  6.76847370E+02  6.45756063E+01  7.57919667E-01  6.14542738E+01  3.56012899E+00
++  1.13252061E+02  1.93248820E+00  1.06173862E+02  7.42992380E+00  1.43076527E+01
++  7.50714425E+02  1.79702257E+01  6.93713186E+02  5.79323581E+01  1.03606917E+02
+   6.99746810E+02  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+   0.00000000E+00  0.00000000E+00  0.00000000E+00  6.53361429E+02  1.82891803E+01
+-  5.99015525E+02  5.44372326E+01  9.40505980E+01  6.14502845E+02  0.00000000E+00
+-  5.31102864E+02  6.77220874E+02  1.53505284E+01  6.26720080E+02  5.08951803E+01
++  5.99562822E+02  5.44372326E+01  9.40505980E+01  6.14502845E+02  0.00000000E+00
++  5.31102864E+02  6.77220874E+02  1.53505284E+01  6.27292689E+02  5.08951803E+01
+   9.21192136E+01  6.29300710E+02  0.00000000E+00  5.55666448E+02  5.64885984E+02
+-  1.36131731E+02  2.59456373E+00  1.26919150E+02  9.41257003E+00  1.76949863E+01
++  1.36131731E+02  2.59456373E+00  1.27035111E+02  9.41257003E+00  1.76949863E+01
+   1.25287818E+02  0.00000000E+00  1.12529845E+02  1.11805549E+02  2.17257828E+01
+-  1.05031585E+02  1.73473071E+00  9.85097219E+01  6.78541827E+00  1.31591746E+01
++  1.05031585E+02  1.73473071E+00  9.85997263E+01  6.78541827E+00  1.31591746E+01
+   9.59185913E+01  0.00000000E+00  8.73413012E+01  8.51921330E+01  1.63092814E+01
+-  1.20953369E+01  1.15327881E+02  2.01792524E+00  1.07908863E+02  7.65648470E+00
++  1.20953369E+01  1.15327881E+02  2.01792524E+00  1.08007455E+02  7.65648470E+00
+   1.46638650E+01  1.05648788E+02  0.00000000E+00  9.56748258E+01  9.40124296E+01
+   1.81057616E+01  1.34932874E+01  1.50233639E+01  1.26451907E+02  2.33864085E+00
+-  1.18043746E+02  8.61880722E+00  1.63092814E+01  1.16187983E+02  0.00000000E+00
++  1.18151598E+02  8.61880722E+00  1.63092814E+01  1.16187983E+02  0.00000000E+00
+   1.04660679E+02  1.03580945E+02  2.00642027E+01  1.50233639E+01  1.66953734E+01
+-  1.85196588E+01  1.28923404E+03  3.87070358E+01  1.17824605E+03  1.11203892E+02
++  1.85196588E+01  1.28923404E+03  3.87070358E+01  1.17932256E+03  1.11203892E+02
+   1.89165096E+02  1.21753341E+03  0.00000000E+00  1.04466382E+03  1.10369829E+03
+   2.25248294E+02  1.75916126E+02  1.92224012E+02  2.09772716E+02  2.04800000E+03
+-  7.37580700E+02  2.06466831E+01  6.76229527E+02  6.14542738E+01  1.06173862E+02
+-  6.93713186E+02  0.00000000E+00  5.99562822E+02  6.27292689E+02  1.27035111E+02
+-  9.85997263E+01  1.08007455E+02  1.18151598E+02  1.17932256E+03  6.76847370E+02
+-  6.53361429E+02  1.82891803E+01  5.99015525E+02  5.44372327E+01  9.40505981E+01
++  8.01323529E+02  2.09604198E+01  7.37580700E+02  6.45756063E+01  1.13252062E+02
++  7.50714426E+02  0.00000000E+00  6.53361429E+02  6.77220874E+02  1.36131731E+02
++  1.05031585E+02  1.15327881E+02  1.26451907E+02  1.28923404E+03  8.01323529E+02
++  6.53361429E+02  1.82891803E+01  5.99562822E+02  5.44372327E+01  9.40505981E+01
+   6.14502846E+02  0.00000000E+00  5.31102864E+02  5.55666449E+02  1.12529845E+02
+-  8.73413013E+01  9.56748257E+01  1.04660679E+02  1.04466382E+03  5.99562822E+02
++  8.73413013E+01  9.56748257E+01  1.04660679E+02  1.04466382E+03  4.00000000E+00
+   5.31102864E+02
+ %FLAG BONDS_INC_HYDROGEN
+ %FORMAT(10I8)
+diff --git a/dat/leap/cmd/leaprc.pol12 b/dat/leap/cmd/leaprc.pol12
+deleted file mode 100644
+index 2bb10c7..0000000
+--- a/dat/leap/cmd/leaprc.pol12
++++ /dev/null
+@@ -1,182 +0,0 @@
+-logFile leap.log
+-#
+-# ----- leaprc for loading pol12, the 2012 pol. force field, no lone pairs
+-#
+-#
+-addAtomTypes {
+-	{ "H"   "H" "sp3" }
+-	{ "HO"  "H" "sp3" }
+-	{ "HS"  "H" "sp3" }
+-	{ "H1"  "H" "sp3" }
+-	{ "H2"  "H" "sp3" }
+-	{ "H3"  "H" "sp3" }
+-	{ "H4"  "H" "sp3" }
+-	{ "H5"  "H" "sp3" }
+-	{ "HW"  "H" "sp3" }
+-	{ "HC"  "H" "sp3" }
+-	{ "HA"  "H" "sp3" }
+-	{ "HP"  "H" "sp3" }
+-	{ "OH"  "O" "sp3" }
+-	{ "OS"  "O" "sp3" }
+-	{ "O"   "O" "sp2" }
+-	{ "O2"  "O" "sp2" }
+-	{ "OW"  "O" "sp3" }
+-	{ "CT"  "C" "sp3" }
+-	{ "CH"  "C" "sp3" }
+-	{ "C2"  "C" "sp3" }
+-	{ "C3"  "C" "sp3" }
+-	{ "C"   "C" "sp2" }
+-	{ "C*"  "C" "sp2" }
+-	{ "CA"  "C" "sp2" }
+-	{ "CB"  "C" "sp2" }
+-	{ "CC"  "C" "sp2" }
+-	{ "CN"  "C" "sp2" }
+-	{ "CM"  "C" "sp2" }
+-	{ "CK"  "C" "sp2" }
+-	{ "CQ"  "C" "sp2" }
+-	{ "CD"  "C" "sp2" }
+-	{ "CE"  "C" "sp2" }
+-	{ "CF"  "C" "sp2" }
+-	{ "CP"  "C" "sp2" }
+-	{ "CI"  "C" "sp2" }
+-	{ "CJ"  "C" "sp2" }
+-	{ "CW"  "C" "sp2" }
+-	{ "CV"  "C" "sp2" }
+-	{ "CR"  "C" "sp2" }
+-	{ "CA"  "C" "sp2" }
+-	{ "CY"  "C" "sp2" }
+-	{ "C0"  "Ca" "sp3" }
+-	{ "MG"  "Mg" "sp3" }
+-	{ "N"   "N" "sp2" }
+-	{ "NA"  "N" "sp2" }
+-	{ "N2"  "N" "sp2" }
+-	{ "N*"  "N" "sp2" }
+-	{ "NP"  "N" "sp2" }
+-	{ "NQ"  "N" "sp2" }
+-	{ "NB"  "N" "sp2" }
+-	{ "NC"  "N" "sp2" }
+-	{ "NT"  "N" "sp3" }
+-	{ "N3"  "N" "sp3" }
+-	{ "S"   "S" "sp3" }
+-	{ "SH"  "S" "sp3" }
+-	{ "P"   "P" "sp3" }
+-	{ "EP"  ""  "sp3" }
+-	{ "F"   "F" "sp3" }
+-	{ "CL"  "Cl" "sp3" }
+-	{ "BR"  "Br" "sp3" }
+-	{ "I"   "I"  "sp3" }
+-	{ "FE"  "Fe" "sp3" }
+-# things should be there
+-        { "IM"  "Cl" "sp3" }
+-        { "IP"  "Na" "sp3" }
+-        { "Li"  "Li"  "sp3" }
+-        { "K"  "K"  "sp3" }
+-        { "Rb"  "Rb"  "sp3" }
+-        { "Cs"  "Cs"  "sp3" }
+-        { "Zn"  "Zn"  "sp3" }
+-        { "IB"  "Na"  "sp3" }
+-# "new" types
+-        { "H0"  "H" "sp3" }
+-
+-}
+-#
+-#	Load the main parameter set.
+-#
+-set default DIPOLE_DAMP_FACTOR 2.5873
+-set default sceescalefactor 1.0
+-set default scnbscalefactor 2.0
+-set default CMAP on
+-
+-parm11 = loadamberparams parmpol12.dat
+-parmpol= loadamberparams frcmod.pol12
+-#
+-#	Load main chain and terminating 
+-#	amino acid libraries.
+-#
+-loadOff aminoctpol12.lib
+-loadOff aminontpol12.lib
+-loadOff aminopol12.lib
+-
+-loadOff ions94.lib
+-loadOff solvents.lib
+-#HOH = TP3
+-#WAT = TP3
+-HOH = PL3
+-WAT = PL3
+-
+-#
+-#	Define the PDB name map for the amino acids and DNA.
+-#
+-addPdbResMap {
+-  { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
+-  { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
+-  { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
+-  { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
+-  { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
+-  { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
+-  { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
+-  { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
+-  { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
+-  { 0 "HID" "NHID" } { 1 "HID" "CHID" }
+-  { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
+-  { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
+-  { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
+-  { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
+-  { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
+-  { 0 "MET" "NMET" } { 1 "MET" "CMET" }
+-  { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
+-  { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
+-  { 0 "SER" "NSER" } { 1 "SER" "CSER" }
+-  { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
+-  { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
+-  { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
+-  { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
+-  { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
+-  { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
+-  { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
+-  { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
+-  { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
+-  { 0 "G" "DG5"  } { 1 "G" "DG3"  } { "G" "DG" } { "GN" "DGN" }
+-  { 0 "A" "DA5"  } { 1 "A" "DA3"  } { "A" "DA" } { "AN" "DAN" }
+-  { 0 "C" "DC5"  } { 1 "C" "DC3"  } { "C" "DC" } { "CN" "DCN" }
+-  { 0 "T" "DT5"  } { 1 "T" "DT3"  } { "T" "DT" } { "TN" "DTN" }
+-  { 0 "C5" "DC5" }
+-  { 0 "G5" "DG5" }
+-  { 0 "A5" "DA5" }
+-  { 0 "T5" "DT5" }
+-  { 1 "C3" "DC3" }
+-  { 1 "G3" "DG3" }
+-  { 1 "A3" "DA3" }
+-  { 1 "T3" "DT3" }
+-
+-}
+-
+-addPdbAtomMap {
+-  { "O5*" "O5'" }
+-  { "C5*" "C5'" }
+-  { "C4*" "C4'" }
+-  { "O4*" "O4'" }
+-  { "C3*" "C3'" }
+-  { "O3*" "O3'" }
+-  { "C2*" "C2'" }
+-  { "C1*" "C1'" }
+-  { "C5M" "C7"  }
+-  { "H1*" "H1'" }
+-  { "H2*1" "H2'1" }
+-  { "H2*2" "H2'2" }
+-  { "H3*" "H3'" }
+-  { "H4*" "H4'" }
+-  { "H5*1" "H5'1" }
+-  { "H5*2" "H5'2" }
+-# old ff atom names -> new
+-  { "O1'" "O4'" }
+-  { "OA"  "O1P" }
+-  { "OB"  "O2P" }
+-}
+-
+-#
+-# assumed that most often proteins use HIE
+-#
+-NHIS = NHIE
+-HIS = HIE
+-CHIS = CHIE
+diff --git a/dat/leap/lib/aminoctpol12.lib b/dat/leap/lib/aminoctpol12.lib
+deleted file mode 100644
+index fa60138..0000000
+--- a/dat/leap/lib/aminoctpol12.lib
++++ /dev/null
+@@ -1,3677 +0,0 @@
+-!!index array str
+- "CALA"
+- "CARG"
+- "CASH"
+- "CASN"
+- "CASP"
+- "CCYM"
+- "CCYS"
+- "CCYX"
+- "CGLH"
+- "CGLN"
+- "CGLU"
+- "CGLY"
+- "CHID"
+- "CHIE"
+- "CHIP"
+- "CILE"
+- "CLEU"
+- "CLYN"
+- "CLYS"
+- "CMET"
+- "CPHE"
+- "CPRO"
+- "CSER"
+- "CTHR"
+- "CTRP"
+- "CTYR"
+- "CVAL"
+- "NME"
+-!entry.CALA.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.139420
+- "HA" "H1" 0 1 131072 4 1 0.100300
+- "CB" "CT" 0 1 131072 5 6 -0.168880
+- "HB1" "HC" 0 1 131072 6 1 0.087020
+- "HB2" "HC" 0 1 131072 7 1 0.087020
+- "HB3" "HC" 0 1 131072 8 1 0.087020
+- "C" "C" 0 1 131072 9 6 0.705530
+- "O" "O2" 0 1 131072 10 8 -0.822990
+- "OXT" "O2" 0 1 131072 11 8 -0.822990
+-!entry.CALA.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB1" "HC" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CALA.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CALA.unit.childsequence single int
+- 2
+-!entry.CALA.unit.connect array int
+- 1
+- 0
+-!entry.CALA.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 9 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 9 10 1
+- 9 11 1
+-!entry.CALA.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+-!entry.CALA.unit.name single str
+- "CALA"
+-!entry.CALA.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 3.877484 3.115795 2.131197
+- 4.075059 4.623017 1.205786
+- 2.496995 3.801075 1.241379
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CALA.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CALA.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CALA" 1 12 1 "p" 0
+-!entry.CALA.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CALA.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CALA.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CARG.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.246160
+- "HA" "H1" 0 1 131072 4 1 0.166180
+- "CB" "CT" 0 1 131072 5 6 0.246480
+- "HB2" "HC" 0 1 131072 6 1 -0.008560
+- "HB3" "HC" 0 1 131072 7 1 -0.008560
+- "CG" "CT" 0 1 131072 8 6 -0.353440
+- "HG2" "HC" 0 1 131072 9 1 0.103290
+- "HG3" "HC" 0 1 131072 10 1 0.103290
+- "CD" "CT" 0 1 131072 11 6 0.608250
+- "HD2" "H1" 0 1 131072 12 1 -0.078660
+- "HD3" "H1" 0 1 131072 13 1 -0.078660
+- "NE" "N2" 0 1 131072 14 7 -0.792460
+- "HE" "H" 0 1 131072 15 1 0.406710
+- "CZ" "CA" 0 1 131072 16 6 1.125120
+- "NH1" "N2" 0 1 131072 17 7 -0.963900
+- "HH11" "H" 0 1 131072 18 1 0.447010
+- "HH12" "H" 0 1 131072 19 1 0.447010
+- "NH2" "N2" 0 1 131072 20 7 -0.963900
+- "HH21" "H" 0 1 131072 21 1 0.447010
+- "HH22" "H" 0 1 131072 22 1 0.447010
+- "C" "C" 0 1 131072 23 6 0.705530
+- "O" "O2" 0 1 131072 24 8 -0.822990
+- "OXT" "O2" 0 1 131072 25 8 -0.822990
+-!entry.CARG.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "H1" 0 -1 0.0
+- "HD3" "H1" 0 -1 0.0
+- "NE" "N2" 0 -1 0.0
+- "HE" "H" 0 -1 0.0
+- "CZ" "CA" 0 -1 0.0
+- "NH1" "N2" 0 -1 0.0
+- "HH11" "H" 0 -1 0.0
+- "HH12" "H" 0 -1 0.0
+- "NH2" "N2" 0 -1 0.0
+- "HH21" "H" 0 -1 0.0
+- "HH22" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CARG.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CARG.unit.childsequence single int
+- 2
+-!entry.CARG.unit.connect array int
+- 1
+- 0
+-!entry.CARG.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 23 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 14 15 1
+- 14 16 1
+- 16 17 1
+- 16 20 1
+- 17 18 1
+- 17 19 1
+- 20 21 1
+- 20 22 1
+- 23 24 1
+- 23 25 1
+-!entry.CARG.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+- "R" 1 "A" 24
+- "R" 1 "A" 25
+-!entry.CARG.unit.name single str
+- "CARG"
+-!entry.CARG.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.881105 5.817645 2.426721
+- 2.801135 5.964881 2.435959
+- 4.181626 5.279602 3.325774
+- 4.540320 7.142723 2.424483
+- 5.151805 7.375492 1.655065
+- 4.364284 8.040989 3.389382
+- 3.575026 7.807606 4.434133
+- 3.088949 6.925423 4.508848
+- 3.465367 8.513631 5.147998
+- 5.006254 9.201287 3.286991
+- 5.604855 9.375325 2.492329
+- 4.892216 9.903045 4.004368
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CARG.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CARG.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CARG" 1 26 1 "p" 0
+-!entry.CARG.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CARG.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CARG.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CASH.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 0.020630
+- "HA" "H1" 0 1 131072 4 1 0.028510
+- "CB" "CT" 0 1 131072 5 6 -0.181320
+- "HB2" "HC" 0 1 131072 6 1 0.139090
+- "HB3" "HC" 0 1 131072 7 1 0.139090
+- "CG" "C" 0 1 131072 8 6 0.590540
+- "OD1" "O" 0 1 131072 9 8 -0.551750
+- "OD2" "OH" 0 1 131072 10 8 -0.583910
+- "HD2" "HO" 0 1 131072 11 1 0.452180
+- "C" "C" 0 1 131072 12 6 0.705530
+- "O" "O2" 0 1 131072 13 8 -0.822990
+- "OXT" "O2" 0 1 131072 14 8 -0.822990
+-!entry.CASH.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C" 0 -1 0.0
+- "OD1" "O" 0 -1 0.0
+- "OD2" "OH" 0 -1 0.0
+- "HD2" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CASH.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CASH.unit.childsequence single int
+- 2
+-!entry.CASH.unit.connect array int
+- 1
+- 0
+-!entry.CASH.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 12 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 10 11 1
+- 12 13 1
+- 12 14 1
+-!entry.CASH.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+-!entry.CASH.unit.name single str
+- "CASH"
+-!entry.CASH.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.275101 5.011380 1.194527
+- 3.669108 5.954940 0.620011
+- 5.407731 5.091879 1.740667
+- 5.742902 5.987179 1.652920
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CASH.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CASH.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CASH" 1 15 1 "p" 0
+-!entry.CASH.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CASH.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CASH.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CASN.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.052240
+- "HA" "H1" 0 1 131072 4 1 0.042740
+- "CB" "CT" 0 1 131072 5 6 -0.207320
+- "HB2" "HC" 0 1 131072 6 1 0.119980
+- "HB3" "HC" 0 1 131072 7 1 0.119980
+- "CG" "C" 0 1 131072 8 6 0.659810
+- "OD1" "O" 0 1 131072 9 8 -0.563050
+- "ND2" "N" 0 1 131072 10 7 -0.856360
+- "HD21" "H" 0 1 131072 11 1 0.394760
+- "HD22" "H" 0 1 131072 12 1 0.394760
+- "C" "C" 0 1 131072 13 6 0.705530
+- "O" "O2" 0 1 131072 14 8 -0.822990
+- "OXT" "O2" 0 1 131072 15 8 -0.822990
+-!entry.CASN.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C" 0 -1 0.0
+- "OD1" "O" 0 -1 0.0
+- "ND2" "N" 0 -1 0.0
+- "HD21" "H" 0 -1 0.0
+- "HD22" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CASN.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CASN.unit.childsequence single int
+- 2
+-!entry.CASN.unit.connect array int
+- 1
+- 0
+-!entry.CASN.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 13 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 10 11 1
+- 10 12 1
+- 13 14 1
+- 13 15 1
+-!entry.CASN.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+-!entry.CASN.unit.name single str
+- "CASN"
+-!entry.CASN.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.253700 5.017112 1.232144
+- 5.005299 5.340406 0.315072
+- 3.984885 5.817909 2.265917
+- 4.408015 6.733702 2.314743
+- 3.359611 5.504297 2.994464
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CASN.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CASN.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CASN" 1 16 1 "p" 0
+-!entry.CASN.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CASN.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CASN.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CASP.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.132120
+- "HA" "H1" 0 1 131072 4 1 0.050730
+- "CB" "CT" 0 1 131072 5 6 -0.282900
+- "HB2" "HC" 0 1 131072 6 1 0.084070
+- "HB3" "HC" 0 1 131072 7 1 0.084070
+- "CG" "C" 0 1 131072 8 6 0.894610
+- "OD1" "O2" 0 1 131072 9 8 -0.822700
+- "OD2" "O2" 0 1 131072 10 8 -0.822700
+- "C" "C" 0 1 131072 11 6 0.705530
+- "O" "O2" 0 1 131072 12 8 -0.822990
+- "OXT" "O2" 0 1 131072 13 8 -0.822990
+-!entry.CASP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C" 0 -1 0.0
+- "OD1" "O2" 0 -1 0.0
+- "OD2" "O2" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CASP.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CASP.unit.childsequence single int
+- 2
+-!entry.CASP.unit.connect array int
+- 1
+- 0
+-!entry.CASP.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 11 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 11 12 1
+- 11 13 1
+-!entry.CASP.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+-!entry.CASP.unit.name single str
+- "CASP"
+-!entry.CASP.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.275101 5.011380 1.194527
+- 3.669108 5.954940 0.620011
+- 5.407731 5.091879 1.740667
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CASP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CASP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CASP" 1 14 1 "p" 0
+-!entry.CASP.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CASP.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CASP.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CCYM.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "HN" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.165660
+- "HA" "H1" 0 1 131072 4 1 0.090680
+- "CB" "CT" 0 1 131072 5 6 0.044510
+- "HB3" "H1" 0 1 131072 6 1 0.006690
+- "HB2" "H1" 0 1 131072 7 1 0.006690
+- "SG" "SH" 0 1 131072 8 16 -0.929850
+- "C" "C" 0 1 131072 9 6 0.705530
+- "O" "O2" 0 1 131072 10 8 -0.822990
+- "OXT" "O2" 0 1 131072 11 8 -0.822990
+-!entry.CCYM.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "HN" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "SG" "SH" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CCYM.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CCYM.unit.childsequence single int
+- 2
+-!entry.CCYM.unit.connect array int
+- 1
+- 0
+-!entry.CCYM.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 9 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 9 10 1
+- 9 11 1
+-!entry.CCYM.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+-!entry.CCYM.unit.name single str
+- "CCYM"
+-!entry.CCYM.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 3.877484 3.115795 2.131197
+- 2.496995 3.801075 1.241379
+- 4.309573 5.303523 1.366036
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CCYM.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CCYM.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CCYM" 1 12 1 "p" 0
+-!entry.CCYM.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CCYM.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CCYM.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CCYS.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.010480
+- "HA" "H1" 0 1 131072 4 1 0.057060
+- "CB" "CT" 0 1 131072 5 6 -0.033990
+- "HB2" "H1" 0 1 131072 6 1 0.066220
+- "HB3" "H1" 0 1 131072 7 1 0.066220
+- "SG" "SH" 0 1 131072 8 16 -0.244870
+- "HG" "HS" 0 1 131072 9 1 0.152900
+- "C" "C" 0 1 131072 10 6 0.705530
+- "O" "O2" 0 1 131072 11 8 -0.822990
+- "OXT" "O2" 0 1 131072 12 8 -0.822990
+-!entry.CCYS.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "SG" "SH" 0 -1 0.0
+- "HG" "HS" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CCYS.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CCYS.unit.childsequence single int
+- 2
+-!entry.CCYS.unit.connect array int
+- 1
+- 0
+-!entry.CCYS.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 10 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 10 11 1
+- 10 12 1
+-!entry.CCYS.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+-!entry.CCYS.unit.name single str
+- "CCYS"
+-!entry.CCYS.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.309573 5.303523 1.366036
+- 3.725392 5.622018 2.517640
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CCYS.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CCYS.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CCYS" 1 13 1 "p" 0
+-!entry.CCYS.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CCYS.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CCYS.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CCYX.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.030070
+- "HA" "H1" 0 1 131072 4 1 0.037000
+- "CB" "CT" 0 1 131072 5 6 -0.043690
+- "HB2" "H1" 0 1 131072 6 1 0.084380
+- "HB3" "H1" 0 1 131072 7 1 0.084380
+- "SG" "S" 0 1 131072 8 16 -0.078940
+- "C" "C" 0 1 131072 9 6 0.705530
+- "O" "O2" 0 1 131072 10 8 -0.822990
+- "OXT" "O2" 0 1 131072 11 8 -0.822990
+-!entry.CCYX.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "SG" "S" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CCYX.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CCYX.unit.childsequence single int
+- 2
+-!entry.CCYX.unit.connect array int
+- 1
+- 0
+-!entry.CCYX.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 9 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 9 10 1
+- 9 11 1
+-!entry.CCYX.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+-!entry.CCYX.unit.name single str
+- "CCYX"
+-!entry.CCYX.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.309573 5.303523 1.366036
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CCYX.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 8 0 0 0
+-!entry.CCYX.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CCYX" 1 12 1 "p" 0
+-!entry.CCYX.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CCYX.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CCYX.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CGLH.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.165080
+- "HA" "H1" 0 1 131072 4 1 0.120280
+- "CB" "CT" 0 1 131072 5 6 0.110660
+- "HB2" "HC" 0 1 131072 6 1 0.016640
+- "HB3" "HC" 0 1 131072 7 1 0.016640
+- "CG" "CT" 0 1 131072 8 6 -0.317930
+- "HG2" "HC" 0 1 131072 9 1 0.173880
+- "HG3" "HC" 0 1 131072 10 1 0.173880
+- "CD" "C" 0 1 131072 11 6 0.664690
+- "OE1" "O" 0 1 131072 12 8 -0.583590
+- "OE2" "OH" 0 1 131072 13 8 -0.613880
+- "HE2" "HO" 0 1 131072 14 1 0.456870
+- "C" "C" 0 1 131072 15 6 0.705530
+- "O" "O2" 0 1 131072 16 8 -0.822990
+- "OXT" "O2" 0 1 131072 17 8 -0.822990
+-!entry.CGLH.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "C" 0 -1 0.0
+- "OE1" "O" 0 -1 0.0
+- "OE2" "OH" 0 -1 0.0
+- "HE2" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CGLH.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CGLH.unit.childsequence single int
+- 2
+-!entry.CGLH.unit.connect array int
+- 1
+- 0
+-!entry.CGLH.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 15 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 15 16 1
+- 15 17 1
+-!entry.CGLH.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+-!entry.CGLH.unit.name single str
+- "CGLH"
+-!entry.CGLH.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.267328 4.996267 1.194946
+- 5.347413 4.849843 1.186158
+- 3.966923 5.535124 0.296342
+- 3.873732 5.805369 2.428706
+- 4.594590 5.679012 3.454376
+- 2.855965 6.542070 2.333721
+- 2.710526 6.996624 3.166684
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CGLH.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CGLH.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CGLH" 1 18 1 "p" 0
+-!entry.CGLH.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CGLH.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CGLH.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CGLN.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.174080
+- "HA" "H1" 0 1 131072 4 1 0.063260
+- "CB" "CT" 0 1 131072 5 6 0.396380
+- "HB2" "HC" 0 1 131072 6 1 -0.058620
+- "HB3" "HC" 0 1 131072 7 1 -0.058620
+- "CG" "CT" 0 1 131072 8 6 -0.593580
+- "HG2" "HC" 0 1 131072 9 1 0.218390
+- "HG3" "HC" 0 1 131072 10 1 0.218390
+- "CD" "C" 0 1 131072 11 6 0.770410
+- "OE1" "O" 0 1 131072 12 8 -0.650910
+- "NE2" "N" 0 1 131072 13 7 -0.874140
+- "HE21" "H" 0 1 131072 14 1 0.398090
+- "HE22" "H" 0 1 131072 15 1 0.398090
+- "C" "C" 0 1 131072 16 6 0.705530
+- "O" "O2" 0 1 131072 17 8 -0.822990
+- "OXT" "O2" 0 1 131072 18 8 -0.822990
+-!entry.CGLN.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "C" 0 -1 0.0
+- "OE1" "O" 0 -1 0.0
+- "NE2" "N" 0 -1 0.0
+- "HE21" "H" 0 -1 0.0
+- "HE22" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CGLN.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CGLN.unit.childsequence single int
+- 2
+-!entry.CGLN.unit.connect array int
+- 1
+- 0
+-!entry.CGLN.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 16 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+- 16 17 1
+- 16 18 1
+-!entry.CGLN.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+-!entry.CGLN.unit.name single str
+- "CGLN"
+-!entry.CGLN.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.906976 5.848443 2.410302
+- 3.138962 5.408349 3.262893
+- 4.458856 7.061523 2.488333
+- 4.248434 7.659045 3.274966
+- 5.084281 7.376210 1.760379
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CGLN.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CGLN.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CGLN" 1 19 1 "p" 0
+-!entry.CGLN.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CGLN.unit.solventcap array dbl
+- -1.000000
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+- 0.0
+- 0.0
+- 0.0
+-!entry.CGLN.unit.velocities table  dbl x  dbl y  dbl z
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+-!entry.CGLU.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.265130
+- "HA" "H1" 0 1 131072 4 1 0.127760
+- "CB" "CT" 0 1 131072 5 6 0.520990
+- "HB2" "HC" 0 1 131072 6 1 -0.129940
+- "HB3" "HC" 0 1 131072 7 1 -0.129940
+- "CG" "CT" 0 1 131072 8 6 -0.693830
+- "HG2" "HC" 0 1 131072 9 1 0.205050
+- "HG3" "HC" 0 1 131072 10 1 0.205050
+- "CD" "C" 0 1 131072 11 6 0.835690
+- "OE1" "O2" 0 1 131072 12 8 -0.811320
+- "OE2" "O2" 0 1 131072 13 8 -0.811320
+- "C" "C" 0 1 131072 14 6 0.705530
+- "O" "O2" 0 1 131072 15 8 -0.822990
+- "OXT" "O2" 0 1 131072 16 8 -0.822990
+-!entry.CGLU.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "C" 0 -1 0.0
+- "OE1" "O2" 0 -1 0.0
+- "OE2" "O2" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CGLU.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CGLU.unit.childsequence single int
+- 2
+-!entry.CGLU.unit.connect array int
+- 1
+- 0
+-!entry.CGLU.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 14 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 14 15 1
+- 14 16 1
+-!entry.CGLU.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+-!entry.CGLU.unit.name single str
+- "CGLU"
+-!entry.CGLU.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.267328 4.996267 1.194946
+- 5.347413 4.849843 1.186158
+- 3.966923 5.535124 0.296342
+- 3.873732 5.805369 2.428706
+- 4.594590 5.679012 3.454376
+- 2.855965 6.542070 2.333721
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CGLU.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CGLU.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CGLU" 1 17 1 "p" 0
+-!entry.CGLU.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CGLU.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CGLU.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CGLY.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.195060
+- "HA2" "H1" 0 1 131072 4 1 0.124060
+- "HA3" "H1" 0 1 131072 5 1 0.124060
+- "C" "C" 0 1 131072 6 6 0.705530
+- "O" "O2" 0 1 131072 7 8 -0.822990
+- "OXT" "O2" 0 1 131072 8 8 -0.822990
+-!entry.CGLY.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA2" "H1" 0 -1 0.0
+- "HA3" "H1" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CGLY.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CGLY.unit.childsequence single int
+- 2
+-!entry.CGLY.unit.connect array int
+- 1
+- 0
+-!entry.CGLY.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 6 1
+- 6 7 1
+- 6 8 1
+-!entry.CGLY.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+-!entry.CGLY.unit.name single str
+- "CGLY"
+-!entry.CGLY.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.671668 3.400125 0.889824
+- 5.483710 2.686702 -4.438857E-06
+- 5.993369 1.568360 -8.469843E-06
+- 6.214748 3.674642 -2.512987E-06
+-!entry.CGLY.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CGLY.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CGLY" 1 9 1 "p" 0
+-!entry.CGLY.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CGLY.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CGLY.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CHID.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.027370
+- "HA" "H1" 0 1 131072 4 1 0.038450
+- "CB" "CT" 0 1 131072 5 6 -0.339570
+- "HB2" "HC" 0 1 131072 6 1 0.133210
+- "HB3" "HC" 0 1 131072 7 1 0.133210
+- "CG" "CC" 0 1 131072 8 6 0.324210
+- "ND1" "NA" 0 1 131072 9 7 -0.387720
+- "HD1" "H" 0 1 131072 10 1 0.367140
+- "CE1" "CR" 0 1 131072 11 6 0.234580
+- "HE1" "H5" 0 1 131072 12 1 0.060770
+- "NE2" "NB" 0 1 131072 13 7 -0.513820
+- "CD2" "CV" 0 1 131072 14 6 -0.060620
+- "HD2" "H4" 0 1 131072 15 1 0.090590
+- "C" "C" 0 1 131072 16 6 0.705530
+- "O" "O2" 0 1 131072 17 8 -0.822990
+- "OXT" "O2" 0 1 131072 18 8 -0.822990
+-!entry.CHID.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CC" 0 -1 0.0
+- "ND1" "NA" 0 -1 0.0
+- "HD1" "H" 0 -1 0.0
+- "CE1" "CR" 0 -1 0.0
+- "HE1" "H5" 0 -1 0.0
+- "NE2" "NB" 0 -1 0.0
+- "CD2" "CV" 0 -1 0.0
+- "HD2" "H4" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CHID.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CHID.unit.childsequence single int
+- 2
+-!entry.CHID.unit.connect array int
+- 1
+- 0
+-!entry.CHID.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 16 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 14 1
+- 9 10 1
+- 9 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 14 15 1
+- 16 17 1
+- 16 18 1
+-!entry.CHID.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+-!entry.CHID.unit.name single str
+- "CHID"
+-!entry.CHID.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.942782 5.885086 2.382972
+- 3.339725 5.691913 3.169805
+- 4.624274 6.997642 2.182500
+- 4.563048 7.811875 2.904563
+- 5.294011 6.891451 1.061663
+- 5.058974 5.678868 0.492453
+- 5.537741 5.417846 -0.451343
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CHID.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CHID.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CHID" 1 19 1 "p" 0
+-!entry.CHID.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CHID.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CHID.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CHIE.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.124850
+- "HA" "H1" 0 1 131072 4 1 0.066680
+- "CB" "CT" 0 1 131072 5 6 -0.261430
+- "HB2" "HC" 0 1 131072 6 1 0.140860
+- "HB3" "HC" 0 1 131072 7 1 0.140860
+- "CG" "CC" 0 1 131072 8 6 0.443190
+- "ND1" "NB" 0 1 131072 9 7 -0.679990
+- "CE1" "CR" 0 1 131072 10 6 0.325720
+- "HE1" "H5" 0 1 131072 11 1 0.037400
+- "NE2" "NA" 0 1 131072 12 7 -0.315320
+- "HE2" "H" 0 1 131072 13 1 0.339080
+- "CD2" "CW" 0 1 131072 14 6 -0.228430
+- "HD2" "H4" 0 1 131072 15 1 0.169290
+- "C" "C" 0 1 131072 16 6 0.705530
+- "O" "O2" 0 1 131072 17 8 -0.822990
+- "OXT" "O2" 0 1 131072 18 8 -0.822990
+-!entry.CHIE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CC" 0 -1 0.0
+- "ND1" "NB" 0 -1 0.0
+- "CE1" "CR" 0 -1 0.0
+- "HE1" "H5" 0 -1 0.0
+- "NE2" "NA" 0 -1 0.0
+- "HE2" "H" 0 -1 0.0
+- "CD2" "CW" 0 -1 0.0
+- "HD2" "H4" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CHIE.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CHIE.unit.childsequence single int
+- 2
+-!entry.CHIE.unit.connect array int
+- 1
+- 0
+-!entry.CHIE.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 16 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
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+- 9 10 1
+- 10 11 1
+- 10 12 1
+- 12 13 1
+- 12 14 1
+- 14 15 1
+- 16 17 1
+- 16 18 1
+-!entry.CHIE.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+-!entry.CHIE.unit.name single str
+- "CHIE"
+-!entry.CHIE.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.942782 5.885086 2.382972
+- 4.624274 6.997642 2.182500
+- 4.563048 7.811875 2.904563
+- 5.294011 6.891451 1.061663
+- 5.896297 7.605085 0.676854
+- 5.058974 5.678868 0.492453
+- 5.537741 5.417846 -0.451343
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CHIE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CHIE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CHIE" 1 19 1 "p" 0
+-!entry.CHIE.unit.residuesPdbSequenceNumber array int
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+-!entry.CHIE.unit.solventcap array dbl
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+-!entry.CHIE.unit.velocities table  dbl x  dbl y  dbl z
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+-!entry.CHIP.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
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+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.029340
+- "HA" "H1" 0 1 131072 4 1 0.065870
+- "CB" "CT" 0 1 131072 5 6 -0.093770
+- "HB2" "HC" 0 1 131072 6 1 0.087980
+- "HB3" "HC" 0 1 131072 7 1 0.087980
+- "CG" "CC" 0 1 131072 8 6 0.263950
+- "ND1" "NA" 0 1 131072 9 7 -0.125480
+- "HD1" "H" 0 1 131072 10 1 0.367860
+- "CE1" "CR" 0 1 131072 11 6 -0.069000
+- "HE1" "H5" 0 1 131072 12 1 0.195860
+- "NE2" "NA" 0 1 131072 13 7 0.034660
+- "HE2" "H" 0 1 131072 14 1 0.297530
+- "CD2" "CW" 0 1 131072 15 6 -0.181280
+- "HD2" "H4" 0 1 131072 16 1 0.150240
+- "C" "C" 0 1 131072 17 6 0.705530
+- "O" "O2" 0 1 131072 18 8 -0.822990
+- "OXT" "O2" 0 1 131072 19 8 -0.822990
+-!entry.CHIP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CC" 0 -1 0.0
+- "ND1" "NA" 0 -1 0.0
+- "HD1" "H" 0 -1 0.0
+- "CE1" "CR" 0 -1 0.0
+- "HE1" "H5" 0 -1 0.0
+- "NE2" "NA" 0 -1 0.0
+- "HE2" "H" 0 -1 0.0
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+- "HD2" "H4" 0 -1 0.0
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+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CHIP.unit.boundbox array dbl
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+- 0.0
+-!entry.CHIP.unit.childsequence single int
+- 2
+-!entry.CHIP.unit.connect array int
+- 1
+- 0
+-!entry.CHIP.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
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+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
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+- 9 10 1
+- 9 11 1
+- 11 12 1
+- 11 13 1
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+- 13 15 1
+- 15 16 1
+- 17 18 1
+- 17 19 1
+-!entry.CHIP.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+-!entry.CHIP.unit.name single str
+- "CHIP"
+-!entry.CHIP.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.942782 5.885086 2.382972
+- 3.339725 5.691913 3.169805
+- 4.624274 6.997642 2.182500
+- 4.563048 7.811875 2.904563
+- 5.294011 6.891451 1.061663
+- 5.896297 7.605085 0.676854
+- 5.058974 5.678868 0.492453
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+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CHIP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CHIP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CHIP" 1 20 1 "p" 0
+-!entry.CHIP.unit.residuesPdbSequenceNumber array int
+- 0
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+-!entry.CHIP.unit.velocities table  dbl x  dbl y  dbl z
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+-!entry.CILE.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.287930
+- "HA" "H1" 0 1 131072 4 1 0.135390
+- "CB" "CT" 0 1 131072 5 6 0.357940
+- "HB" "HC" 0 1 131072 6 1 -0.079320
+- "CG2" "CT" 0 1 131072 7 6 -0.501190
+- "HG21" "HC" 0 1 131072 8 1 0.140430
+- "HG22" "HC" 0 1 131072 9 1 0.140430
+- "HG23" "HC" 0 1 131072 10 1 0.140430
+- "CG1" "CT" 0 1 131072 11 6 -0.081150
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+- "HG13" "HC" 0 1 131072 13 1 0.048560
+- "CD1" "CT" 0 1 131072 14 6 -0.094950
+- "HD11" "HC" 0 1 131072 15 1 0.028620
+- "HD12" "HC" 0 1 131072 16 1 0.028620
+- "HD13" "HC" 0 1 131072 17 1 0.028620
+- "C" "C" 0 1 131072 18 6 0.705530
+- "O" "O2" 0 1 131072 19 8 -0.822990
+- "OXT" "O2" 0 1 131072 20 8 -0.822990
+-!entry.CILE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB" "HC" 0 -1 0.0
+- "CG2" "CT" 0 -1 0.0
+- "HG21" "HC" 0 -1 0.0
+- "HG22" "HC" 0 -1 0.0
+- "HG23" "HC" 0 -1 0.0
+- "CG1" "CT" 0 -1 0.0
+- "HG12" "HC" 0 -1 0.0
+- "HG13" "HC" 0 -1 0.0
+- "CD1" "CT" 0 -1 0.0
+- "HD11" "HC" 0 -1 0.0
+- "HD12" "HC" 0 -1 0.0
+- "HD13" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CILE.unit.boundbox array dbl
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+- 0.0
+-!entry.CILE.unit.childsequence single int
+- 2
+-!entry.CILE.unit.connect array int
+- 1
+- 0
+-!entry.CILE.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 18 1
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+- 5 7 1
+- 5 11 1
+- 7 8 1
+- 7 9 1
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+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 14 15 1
+- 14 16 1
+- 14 17 1
+- 18 19 1
+- 18 20 1
+-!entry.CILE.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
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+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+-!entry.CILE.unit.name single str
+- "CILE"
+-!entry.CILE.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
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+- 4.230204 4.986694 1.245169
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+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CILE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CILE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CILE" 1 21 1 "p" 0
+-!entry.CILE.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CILE.unit.solventcap array dbl
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+-!entry.CILE.unit.velocities table  dbl x  dbl y  dbl z
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+-!entry.CLEU.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.151630
+- "HA" "H1" 0 1 131072 4 1 0.080730
+- "CB" "CT" 0 1 131072 5 6 -0.251240
+- "HB2" "HC" 0 1 131072 6 1 0.113740
+- "HB3" "HC" 0 1 131072 7 1 0.113740
+- "CG" "CT" 0 1 131072 8 6 0.579270
+- "HG" "HC" 0 1 131072 9 1 -0.096890
+- "CD1" "CT" 0 1 131072 10 6 -0.760610
+- "HD11" "HC" 0 1 131072 11 1 0.197760
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+- "HD13" "HC" 0 1 131072 13 1 0.197760
+- "CD2" "CT" 0 1 131072 14 6 -0.760610
+- "HD21" "HC" 0 1 131072 15 1 0.197760
+- "HD22" "HC" 0 1 131072 16 1 0.197760
+- "HD23" "HC" 0 1 131072 17 1 0.197760
+- "C" "C" 0 1 131072 18 6 0.705530
+- "O" "O2" 0 1 131072 19 8 -0.822990
+- "OXT" "O2" 0 1 131072 20 8 -0.822990
+-!entry.CLEU.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG" "HC" 0 -1 0.0
+- "CD1" "CT" 0 -1 0.0
+- "HD11" "HC" 0 -1 0.0
+- "HD12" "HC" 0 -1 0.0
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+- "CD2" "CT" 0 -1 0.0
+- "HD21" "HC" 0 -1 0.0
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+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CLEU.unit.boundbox array dbl
+- -1.000000
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+- 0.0
+-!entry.CLEU.unit.childsequence single int
+- 2
+-!entry.CLEU.unit.connect array int
+- 1
+- 0
+-!entry.CLEU.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 18 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
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+- 10 11 1
+- 10 12 1
+- 10 13 1
+- 14 15 1
+- 14 16 1
+- 14 17 1
+- 18 19 1
+- 18 20 1
+-!entry.CLEU.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+-!entry.CLEU.unit.name single str
+- "CLEU"
+-!entry.CLEU.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
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+- 4.274186 5.009602 1.194577
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+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CLEU.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CLEU.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CLEU" 1 21 1 "p" 0
+-!entry.CLEU.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CLEU.unit.solventcap array dbl
+- -1.000000
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+-!entry.CLEU.unit.velocities table  dbl x  dbl y  dbl z
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+-!entry.CLYN.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.163200
+- "HA" "H1" 0 1 131072 4 1 0.095860
+- "CB" "CT" 0 1 131072 5 6 0.095690
+- "HB2" "HC" 0 1 131072 6 1 -0.015960
+- "HB3" "HC" 0 1 131072 7 1 -0.015960
+- "CG" "CT" 0 1 131072 8 6 0.018310
+- "HG2" "HC" 0 1 131072 9 1 0.010750
+- "HG3" "HC" 0 1 131072 10 1 0.010750
+- "CD" "CT" 0 1 131072 11 6 -0.229410
+- "HD2" "HC" 0 1 131072 12 1 0.104310
+- "HD3" "HC" 0 1 131072 13 1 0.104310
+- "CE" "CT" 0 1 131072 14 6 0.528910
+- "HE2" "H1" 0 1 131072 15 1 -0.110750
+- "HE3" "H1" 0 1 131072 16 1 -0.110750
+- "NZ" "NT" 0 1 131072 17 7 -0.980200
+- "HZ2" "H" 0 1 131072 18 1 0.355200
+- "HZ3" "H" 0 1 131072 19 1 0.355200
+- "C" "C" 0 1 131072 20 6 0.705530
+- "O" "O2" 0 1 131072 21 8 -0.822990
+- "OXT" "O2" 0 1 131072 22 8 -0.822990
+-!entry.CLYN.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
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+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "HC" 0 -1 0.0
+- "HD3" "HC" 0 -1 0.0
+- "CE" "CT" 0 -1 0.0
+- "HE2" "H1" 0 -1 0.0
+- "HE3" "H1" 0 -1 0.0
+- "NZ" "NT" 0 -1 0.0
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+- "HZ3" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CLYN.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CLYN.unit.childsequence single int
+- 2
+-!entry.CLYN.unit.connect array int
+- 1
+- 0
+-!entry.CLYN.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 20 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 14 15 1
+- 14 16 1
+- 14 17 1
+- 17 18 1
+- 17 19 1
+- 20 21 1
+- 20 22 1
+-!entry.CLYN.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+-!entry.CLYN.unit.name single str
+- "CLYN"
+-!entry.CLYN.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.881105 5.817645 2.426721
+- 2.801135 5.964881 2.435959
+- 4.181626 5.279602 3.325774
+- 4.578325 7.173410 2.389153
+- 5.658410 7.026987 2.380363
+- 4.277917 7.712267 1.490550
+- 4.199422 7.952309 3.576860
+- 4.661186 8.850226 3.551979
+- 3.198675 8.088466 3.584971
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CLYN.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CLYN.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CLYN" 1 23 1 "p" 0
+-!entry.CLYN.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CLYN.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CLYN.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CLYS.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.185190
+- "HA" "H1" 0 1 131072 4 1 0.120990
+- "CB" "CT" 0 1 131072 5 6 0.035190
+- "HB2" "HC" 0 1 131072 6 1 0.015850
+- "HB3" "HC" 0 1 131072 7 1 0.015850
+- "CG" "CT" 0 1 131072 8 6 -0.039190
+- "HG2" "HC" 0 1 131072 9 1 0.047540
+- "HG3" "HC" 0 1 131072 10 1 0.047540
+- "CD" "CT" 0 1 131072 11 6 -0.190030
+- "HD2" "HC" 0 1 131072 12 1 0.094440
+- "HD3" "HC" 0 1 131072 13 1 0.094440
+- "CE" "CT" 0 1 131072 14 6 0.457400
+- "HE2" "HP" 0 1 131072 15 1 -0.049110
+- "HE3" "HP" 0 1 131072 16 1 -0.049110
+- "NZ" "N3" 0 1 131072 17 7 -0.371640
+- "HZ1" "H" 0 1 131072 18 1 0.336030
+- "HZ2" "H" 0 1 131072 19 1 0.336030
+- "HZ3" "H" 0 1 131072 20 1 0.336030
+- "C" "C" 0 1 131072 21 6 0.705530
+- "O" "O2" 0 1 131072 22 8 -0.822990
+- "OXT" "O2" 0 1 131072 23 8 -0.822990
+-!entry.CLYS.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "HC" 0 -1 0.0
+- "HD3" "HC" 0 -1 0.0
+- "CE" "CT" 0 -1 0.0
+- "HE2" "HP" 0 -1 0.0
+- "HE3" "HP" 0 -1 0.0
+- "NZ" "N3" 0 -1 0.0
+- "HZ1" "H" 0 -1 0.0
+- "HZ2" "H" 0 -1 0.0
+- "HZ3" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CLYS.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CLYS.unit.childsequence single int
+- 2
+-!entry.CLYS.unit.connect array int
+- 1
+- 0
+-!entry.CLYS.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 21 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 14 15 1
+- 14 16 1
+- 14 17 1
+- 17 18 1
+- 17 19 1
+- 17 20 1
+- 21 22 1
+- 21 23 1
+-!entry.CLYS.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+-!entry.CLYS.unit.name single str
+- "CLYS"
+-!entry.CLYS.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.881105 5.817645 2.426721
+- 2.801135 5.964881 2.435959
+- 4.181626 5.279602 3.325774
+- 4.578325 7.173410 2.389153
+- 5.658410 7.026987 2.380363
+- 4.277917 7.712267 1.490550
+- 4.199422 7.952309 3.576860
+- 4.478085 7.453366 4.409628
+- 4.661186 8.850226 3.551979
+- 3.198675 8.088466 3.584971
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CLYS.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CLYS.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CLYS" 1 24 1 "p" 0
+-!entry.CLYS.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CLYS.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CLYS.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CMET.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.171820
+- "HA" "H1" 0 1 131072 4 1 0.129660
+- "CB" "CT" 0 1 131072 5 6 0.250160
+- "HB2" "HC" 0 1 131072 6 1 -0.026630
+- "HB3" "HC" 0 1 131072 7 1 -0.026630
+- "CG" "CT" 0 1 131072 8 6 -0.366710
+- "HG2" "H1" 0 1 131072 9 1 0.160270
+- "HG3" "H1" 0 1 131072 10 1 0.160270
+- "SD" "S" 0 1 131072 11 16 -0.122120
+- "CE" "CT" 0 1 131072 12 6 -0.263690
+- "HE1" "H1" 0 1 131072 13 1 0.110100
+- "HE2" "H1" 0 1 131072 14 1 0.110100
+- "HE3" "H1" 0 1 131072 15 1 0.110100
+- "C" "C" 0 1 131072 16 6 0.705530
+- "O" "O2" 0 1 131072 17 8 -0.822990
+- "OXT" "O2" 0 1 131072 18 8 -0.822990
+-!entry.CMET.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "H1" 0 -1 0.0
+- "HG3" "H1" 0 -1 0.0
+- "SD" "S" 0 -1 0.0
+- "CE" "CT" 0 -1 0.0
+- "HE1" "H1" 0 -1 0.0
+- "HE2" "H1" 0 -1 0.0
+- "HE3" "H1" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CMET.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CMET.unit.childsequence single int
+- 2
+-!entry.CMET.unit.connect array int
+- 1
+- 0
+-!entry.CMET.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 16 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 12 13 1
+- 12 14 1
+- 12 15 1
+- 16 17 1
+- 16 18 1
+-!entry.CMET.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+-!entry.CMET.unit.name single str
+- "CMET"
+-!entry.CMET.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.817309 5.981266 2.651708
+- 4.753212 7.463128 2.340949
+- 4.433582 7.904044 1.396741
+- 4.585907 8.175299 3.148985
+- 5.814074 7.218763 2.286554
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CMET.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CMET.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CMET" 1 19 1 "p" 0
+-!entry.CMET.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CMET.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CMET.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CPHE.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.072690
+- "HA" "H1" 0 1 131072 4 1 0.053080
+- "CB" "CT" 0 1 131072 5 6 -0.213480
+- "HB2" "HC" 0 1 131072 6 1 0.116210
+- "HB3" "HC" 0 1 131072 7 1 0.116210
+- "CG" "CA" 0 1 131072 8 6 0.197950
+- "CD1" "CA" 0 1 131072 9 6 -0.219910
+- "HD1" "HA" 0 1 131072 10 1 0.142120
+- "CE1" "CA" 0 1 131072 11 6 -0.084720
+- "HE1" "HA" 0 1 131072 12 1 0.108500
+- "CZ" "CA" 0 1 131072 13 6 -0.128160
+- "HZ" "HA" 0 1 131072 14 1 0.091960
+- "CE2" "CA" 0 1 131072 15 6 -0.084720
+- "HE2" "HA" 0 1 131072 16 1 0.108500
+- "CD2" "CA" 0 1 131072 17 6 -0.219910
+- "HD2" "HA" 0 1 131072 18 1 0.142120
+- "C" "C" 0 1 131072 19 6 0.705530
+- "O" "O2" 0 1 131072 20 8 -0.822990
+- "OXT" "O2" 0 1 131072 21 8 -0.822990
+-!entry.CPHE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CA" 0 -1 0.0
+- "CD1" "CA" 0 -1 0.0
+- "HD1" "HA" 0 -1 0.0
+- "CE1" "CA" 0 -1 0.0
+- "HE1" "HA" 0 -1 0.0
+- "CZ" "CA" 0 -1 0.0
+- "HZ" "HA" 0 -1 0.0
+- "CE2" "CA" 0 -1 0.0
+- "HE2" "HA" 0 -1 0.0
+- "CD2" "CA" 0 -1 0.0
+- "HD2" "HA" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CPHE.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CPHE.unit.childsequence single int
+- 2
+-!entry.CPHE.unit.connect array int
+- 1
+- 0
+-!entry.CPHE.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 19 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 17 1
+- 9 10 1
+- 9 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+- 15 17 1
+- 17 18 1
+- 19 20 1
+- 19 21 1
+-!entry.CPHE.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+-!entry.CPHE.unit.name single str
+- "CPHE"
+-!entry.CPHE.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.911613 5.857250 2.409890
+- 3.236123 5.513843 3.193398
+- 4.490014 7.129513 2.492354
+- 4.264853 7.776651 3.340066
+- 5.357616 7.570591 1.486016
+- 5.807943 8.561138 1.550220
+- 5.646818 6.739407 0.397211
+- 6.322309 7.082817 -0.386295
+- 5.068419 5.467143 0.314744
+- 5.293584 4.820007 -0.532968
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CPHE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CPHE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CPHE" 1 22 1 "p" 0
+-!entry.CPHE.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CPHE.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CPHE.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CPRO.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.251210
+- "CD" "CT" 0 1 131072 2 6 0.062560
+- "HD2" "H1" 0 1 131072 3 1 0.022030
+- "HD3" "H1" 0 1 131072 4 1 0.022010
+- "CG" "CT" 0 1 131072 5 6 0.066380
+- "HG2" "HC" 0 1 131072 6 1 0.007490
+- "HG3" "HC" 0 1 131072 7 1 0.007490
+- "CB" "CT" 0 1 131072 8 6 0.069820
+- "HB2" "HC" 0 1 131072 9 1 0.013210
+- "HB3" "HC" 0 1 131072 10 1 0.013210
+- "CA" "CT" 0 1 131072 11 6 -0.200450
+- "HA" "H1" 0 1 131072 12 1 0.107910
+- "C" "C" 0 1 131072 13 6 0.705530
+- "O" "O2" 0 1 131072 14 8 -0.822990
+- "OXT" "O2" 0 1 131072 15 8 -0.822990
+-!entry.CPRO.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "H1" 0 -1 0.0
+- "HD3" "H1" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CPRO.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CPRO.unit.childsequence single int
+- 2
+-!entry.CPRO.unit.connect array int
+- 1
+- 0
+-!entry.CPRO.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 11 1
+- 2 3 1
+- 2 4 1
+- 2 5 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+-!entry.CPRO.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+-!entry.CPRO.unit.name single str
+- "CPRO"
+-!entry.CPRO.unit.positions table  dbl x  dbl y  dbl z
+- 3.326834 1.557389 -1.603945E-06
+- 4.302147 0.476598 0.080119
+- 4.419998 0.019283 -0.902263
+- 3.955888 -0.274040 0.790574
+- 5.547126 1.172441 0.544693
+- 6.413549 0.741636 0.042879
+- 5.652950 1.047934 1.622376
+- 5.369091 2.628184 0.185227
+- 5.969289 2.861861 -0.694123
+- 5.690642 3.251038 1.019947
+- 3.933610 2.871277 -0.104508
+- 3.611470 3.488570 0.734106
+- 3.505164 3.526392 -1.409783
+- 2.754240 2.939065 -2.185412
+- 3.904907 4.650696 -1.704043
+-!entry.CPRO.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CPRO.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CPRO" 1 16 1 "p" 0
+-!entry.CPRO.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CPRO.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CPRO.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+-!entry.CSER.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.069940
+- "HA" "H1" 0 1 131072 4 1 0.110000
+- "CB" "CT" 0 1 131072 5 6 0.169960
+- "HB2" "H1" 0 1 131072 6 1 0.022900
+- "HB3" "H1" 0 1 131072 7 1 0.022900
+- "OG" "OH" 0 1 131072 8 8 -0.571310
+- "HG" "HO" 0 1 131072 9 1 0.368550
+- "C" "C" 0 1 131072 10 6 0.705530
+- "O" "O2" 0 1 131072 11 8 -0.822990
+- "OXT" "O2" 0 1 131072 12 8 -0.822990
+-!entry.CSER.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "OG" "OH" 0 -1 0.0
+- "HG" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CSER.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CSER.unit.childsequence single int
+- 2
+-!entry.CSER.unit.connect array int
+- 1
+- 0
+-!entry.CSER.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 10 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 10 11 1
+- 10 12 1
+-!entry.CSER.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+-!entry.CSER.unit.name single str
+- "CSER"
+-!entry.CSER.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.230753 4.925145 1.196917
+- 3.983305 5.433814 1.972562
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CSER.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CSER.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CSER" 1 13 1 "p" 0
+-!entry.CSER.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CSER.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CSER.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+-!entry.CTHR.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 0.019110
+- "HA" "H1" 0 1 131072 4 1 0.067720
+- "CB" "CT" 0 1 131072 5 6 0.444500
+- "HB" "H1" 0 1 131072 6 1 -0.106110
+- "CG2" "CT" 0 1 131072 7 6 -0.496090
+- "HG21" "HC" 0 1 131072 8 1 0.133070
+- "HG22" "HC" 0 1 131072 9 1 0.133070
+- "HG23" "HC" 0 1 131072 10 1 0.133070
+- "OG1" "OH" 0 1 131072 11 8 -0.724290
+- "HG1" "HO" 0 1 131072 12 1 0.449010
+- "C" "C" 0 1 131072 13 6 0.705530
+- "O" "O2" 0 1 131072 14 8 -0.822990
+- "OXT" "O2" 0 1 131072 15 8 -0.822990
+-!entry.CTHR.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB" "H1" 0 -1 0.0
+- "CG2" "CT" 0 -1 0.0
+- "HG21" "HC" 0 -1 0.0
+- "HG22" "HC" 0 -1 0.0
+- "HG23" "HC" 0 -1 0.0
+- "OG1" "OH" 0 -1 0.0
+- "HG1" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CTHR.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CTHR.unit.childsequence single int
+- 2
+-!entry.CTHR.unit.connect array int
+- 1
+- 0
+-!entry.CTHR.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 13 1
+- 5 6 1
+- 5 7 1
+- 5 11 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 11 12 1
+- 13 14 1
+- 13 15 1
+-!entry.CTHR.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+-!entry.CTHR.unit.name single str
+- "CTHR"
+-!entry.CTHR.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 4.075059 4.623017 1.205786
+- 2.065936 3.859425 1.244383
+- 1.567127 2.890627 1.271209
+- 1.784431 4.436953 2.124903
+- 1.764699 4.397847 0.345796
+- 3.971501 2.947413 2.411212
+- 3.724052 3.456082 3.186857
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CTHR.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CTHR.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CTHR" 1 16 1 "p" 0
+-!entry.CTHR.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CTHR.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CTHR.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CTRP.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.090040
+- "HA" "H1" 0 1 131072 4 1 0.084020
+- "CB" "CT" 0 1 131072 5 6 0.040520
+- "HB2" "HC" 0 1 131072 6 1 0.031680
+- "HB3" "HC" 0 1 131072 7 1 0.031680
+- "CG" "C*" 0 1 131072 8 6 -0.293840
+- "CD1" "CW" 0 1 131072 9 6 0.036620
+- "HD1" "H4" 0 1 131072 10 1 0.130250
+- "NE1" "NA" 0 1 131072 11 7 -0.473000
+- "HE1" "H" 0 1 131072 12 1 0.391490
+- "CE2" "CN" 0 1 131072 13 6 0.187500
+- "CZ2" "CA" 0 1 131072 14 6 -0.261570
+- "HZ2" "HA" 0 1 131072 15 1 0.183290
+- "CH2" "CA" 0 1 131072 16 6 -0.178280
+- "HH2" "HA" 0 1 131072 17 1 0.106010
+- "CZ3" "CA" 0 1 131072 18 6 -0.048150
+- "HZ3" "HA" 0 1 131072 19 1 0.086830
+- "CE3" "CA" 0 1 131072 20 6 -0.414910
+- "HE3" "HA" 0 1 131072 21 1 0.219040
+- "CD2" "CB" 0 1 131072 22 6 0.283920
+- "C" "C" 0 1 131072 23 6 0.705530
+- "O" "O2" 0 1 131072 24 8 -0.822990
+- "OXT" "O2" 0 1 131072 25 8 -0.822990
+-!entry.CTRP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C*" 0 -1 0.0
+- "CD1" "CW" 0 -1 0.0
+- "HD1" "H4" 0 -1 0.0
+- "NE1" "NA" 0 -1 0.0
+- "HE1" "H" 0 -1 0.0
+- "CE2" "CN" 0 -1 0.0
+- "CZ2" "CA" 0 -1 0.0
+- "HZ2" "HA" 0 -1 0.0
+- "CH2" "CA" 0 -1 0.0
+- "HH2" "HA" 0 -1 0.0
+- "CZ3" "CA" 0 -1 0.0
+- "HZ3" "HA" 0 -1 0.0
+- "CE3" "CA" 0 -1 0.0
+- "HE3" "HA" 0 -1 0.0
+- "CD2" "CB" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CTRP.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CTRP.unit.childsequence single int
+- 2
+-!entry.CTRP.unit.connect array int
+- 1
+- 0
+-!entry.CTRP.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 23 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 22 1
+- 9 10 1
+- 9 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 22 1
+- 14 15 1
+- 14 16 1
+- 16 17 1
+- 16 18 1
+- 18 19 1
+- 18 20 1
+- 20 21 1
+- 20 22 1
+- 23 24 1
+- 23 25 1
+-!entry.CTRP.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+- "R" 1 "A" 24
+- "R" 1 "A" 25
+-!entry.CTRP.unit.name single str
+- "CTRP"
+-!entry.CTRP.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 4.023453 5.931084 2.293240
+- 3.368841 5.705466 3.135071
+- 4.811943 7.073555 1.949808
+- 4.882921 7.922010 2.493118
+- 5.427347 6.842060 0.816764
+- 6.297161 7.689052 0.119605
+- 6.531230 8.676649 0.517050
+- 6.814091 7.187011 -1.069023
+- 7.498074 7.791857 -1.664362
+- 6.482659 5.953119 -1.505101
+- 6.897660 5.575648 -2.439654
+- 5.604041 5.117355 -0.785636
+- 5.358720 4.126570 -1.168080
+- 5.083390 5.623004 0.411545
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CTRP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CTRP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CTRP" 1 26 1 "p" 0
+-!entry.CTRP.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CTRP.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CTRP.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CTYR.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.175550
+- "HA" "H1" 0 1 131072 4 1 0.121890
+- "CB" "CT" 0 1 131072 5 6 -0.093730
+- "HB2" "HC" 0 1 131072 6 1 0.086440
+- "HB3" "HC" 0 1 131072 7 1 0.086440
+- "CG" "CA" 0 1 131072 8 6 0.017450
+- "CD1" "CA" 0 1 131072 9 6 -0.128300
+- "HD1" "HA" 0 1 131072 10 1 0.137650
+- "CE1" "CA" 0 1 131072 11 6 -0.334250
+- "HE1" "HA" 0 1 131072 12 1 0.190120
+- "CZ" "CA" 0 1 131072 13 6 0.442000
+- "OH" "OH" 0 1 131072 14 8 -0.544620
+- "HH" "HO" 0 1 131072 15 1 0.382300
+- "CE2" "CA" 0 1 131072 16 6 -0.334250
+- "HE2" "HA" 0 1 131072 17 1 0.190120
+- "CD2" "CA" 0 1 131072 18 6 -0.128300
+- "HD2" "HA" 0 1 131072 19 1 0.137650
+- "C" "C" 0 1 131072 20 6 0.705530
+- "O" "O2" 0 1 131072 21 8 -0.822990
+- "OXT" "O2" 0 1 131072 22 8 -0.822990
+-!entry.CTYR.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CA" 0 -1 0.0
+- "CD1" "CA" 0 -1 0.0
+- "HD1" "HA" 0 -1 0.0
+- "CE1" "CA" 0 -1 0.0
+- "HE1" "HA" 0 -1 0.0
+- "CZ" "CA" 0 -1 0.0
+- "OH" "OH" 0 -1 0.0
+- "HH" "HO" 0 -1 0.0
+- "CE2" "CA" 0 -1 0.0
+- "HE2" "HA" 0 -1 0.0
+- "CD2" "CA" 0 -1 0.0
+- "HD2" "HA" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CTYR.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CTYR.unit.childsequence single int
+- 2
+-!entry.CTYR.unit.connect array int
+- 1
+- 0
+-!entry.CTYR.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 20 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 18 1
+- 9 10 1
+- 9 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 16 1
+- 14 15 1
+- 16 17 1
+- 16 18 1
+- 18 19 1
+- 20 21 1
+- 20 22 1
+-!entry.CTYR.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+-!entry.CTYR.unit.name single str
+- "CTYR"
+-!entry.CTYR.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.267328 4.996267 1.194946
+- 4.059927 5.918911 2.227280
+- 3.400108 5.668218 3.057877
+- 4.699998 7.163547 2.192791
+- 4.538522 7.881891 2.996538
+- 5.547471 7.485542 1.125970
+- 6.169255 8.694617 1.092468
+- 5.956327 9.246984 1.848214
+- 5.754875 6.562900 0.093635
+- 6.414694 6.813595 -0.736962
+- 5.114806 5.318263 0.128119
+- 5.276286 4.599920 -0.675627
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CTYR.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CTYR.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CTYR" 1 23 1 "p" 0
+-!entry.CTYR.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CTYR.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CTYR.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CVAL.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.213060
+- "HA" "H1" 0 1 131072 4 1 0.122010
+- "CB" "CT" 0 1 131072 5 6 0.550920
+- "HB" "HC" 0 1 131072 6 1 -0.083650
+- "CG1" "CT" 0 1 131072 7 6 -0.705720
+- "HG11" "HC" 0 1 131072 8 1 0.181380
+- "HG12" "HC" 0 1 131072 9 1 0.181380
+- "HG13" "HC" 0 1 131072 10 1 0.181380
+- "CG2" "CT" 0 1 131072 11 6 -0.705720
+- "HG21" "HC" 0 1 131072 12 1 0.181380
+- "HG22" "HC" 0 1 131072 13 1 0.181380
+- "HG23" "HC" 0 1 131072 14 1 0.181380
+- "C" "C" 0 1 131072 15 6 0.705530
+- "O" "O2" 0 1 131072 16 8 -0.822990
+- "OXT" "O2" 0 1 131072 17 8 -0.822990
+-!entry.CVAL.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB" "HC" 0 -1 0.0
+- "CG1" "CT" 0 -1 0.0
+- "HG11" "HC" 0 -1 0.0
+- "HG12" "HC" 0 -1 0.0
+- "HG13" "HC" 0 -1 0.0
+- "CG2" "CT" 0 -1 0.0
+- "HG21" "HC" 0 -1 0.0
+- "HG22" "HC" 0 -1 0.0
+- "HG23" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O2" 0 -1 0.0
+- "OXT" "O2" 0 -1 0.0
+-!entry.CVAL.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CVAL.unit.childsequence single int
+- 2
+-!entry.CVAL.unit.connect array int
+- 1
+- 0
+-!entry.CVAL.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 15 1
+- 5 6 1
+- 5 7 1
+- 5 11 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 15 16 1
+- 15 17 1
+-!entry.CVAL.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+-!entry.CVAL.unit.name single str
+- "CVAL"
+-!entry.CVAL.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.997712 2.900483 2.489542
+- 5.077693 2.753265 2.481244
+- 3.716972 3.477628 3.370558
+- 3.499630 1.931323 2.516834
+- 4.274186 5.009602 1.194577
+- 3.973781 5.548460 0.295972
+- 3.993559 5.587585 2.075079
+- 5.354271 4.863178 1.185788
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+- 6.204455 3.702003 -2.420005E-06
+-!entry.CVAL.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 0 0 0 0 0
+-!entry.CVAL.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CVAL" 1 18 1 "p" 0
+-!entry.CVAL.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CVAL.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CVAL.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NME.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.534190
+- "H" "H" 0 1 131072 2 1 0.339300
+- "CH3" "CT" 0 1 131072 3 6 0.044800
+- "HH31" "H1" 0 1 131072 4 1 0.050030
+- "HH32" "H1" 0 1 131072 5 1 0.050030
+- "HH33" "H1" 0 1 131072 6 1 0.050030
+-!entry.NME.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CH3" "CT" 0 -1 0.0
+- "HH31" "H1" 0 -1 0.0
+- "HH32" "H1" 0 -1 0.0
+- "HH33" "H1" 0 -1 0.0
+-!entry.NME.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NME.unit.childsequence single int
+- 2
+-!entry.NME.unit.connect array int
+- 1
+- 0
+-!entry.NME.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 6 1
+-!entry.NME.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+-!entry.NME.unit.name single str
+- "NME"
+-!entry.NME.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.211504 3.628554 2.348065E-06
+- 4.591993 2.943271 0.889822
+- 4.591988 2.943275 -0.889825
+-!entry.NME.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 3 0 0 0 0
+-!entry.NME.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NME" 1 7 1 "p" 0
+-!entry.NME.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NME.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NME.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+diff --git a/dat/leap/lib/aminontpol12.lib b/dat/leap/lib/aminontpol12.lib
+deleted file mode 100644
+index ead0d89..0000000
+--- a/dat/leap/lib/aminontpol12.lib
++++ /dev/null
+@@ -1,3839 +0,0 @@
+-!!index array str
+- "ACE"
+- "NALA"
+- "NARG"
+- "NASH"
+- "NASN"
+- "NASP"
+- "NCYM"
+- "NCYS"
+- "NCYX"
+- "NGLH"
+- "NGLN"
+- "NGLU"
+- "NGLY"
+- "NHID"
+- "NHIE"
+- "NHIP"
+- "NILE"
+- "NLEU"
+- "NLYN"
+- "NLYS"
+- "NMET"
+- "NPHE"
+- "NPRO"
+- "NSER"
+- "NTHR"
+- "NTRP"
+- "NTYR"
+- "NVAL"
+-!entry.ACE.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "HH31" "HC" 0 1 131072 1 1 0.245320
+- "CH3" "CT" 0 1 131072 2 6 -0.841920
+- "HH32" "HC" 0 1 131072 3 1 0.245320
+- "HH33" "HC" 0 1 131072 4 1 0.245320
+- "C" "C" 0 1 131072 5 6 0.730100
+- "O" "O" 0 1 131072 6 8 -0.624140
+-!entry.ACE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "HH31" "HC" 0 -1 0.0
+- "CH3" "CT" 0 -1 0.0
+- "HH32" "HC" 0 -1 0.0
+- "HH33" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.ACE.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ACE.unit.childsequence single int
+- 2
+-!entry.ACE.unit.connect array int
+- 0
+- 5
+-!entry.ACE.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 2 3 1
+- 2 4 1
+- 2 5 1
+- 5 6 1
+-!entry.ACE.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+-!entry.ACE.unit.name single str
+- "ACE"
+-!entry.ACE.unit.positions table  dbl x  dbl y  dbl z
+- 2.000001 1.000000 -1.346410E-06
+- 2.000001 2.090000 1.211769E-07
+- 1.486264 2.453849 0.889824
+- 1.486259 2.453852 -0.889820
+- 3.427420 2.640795 -2.981008E-06
+- 4.390580 1.877406 -6.602402E-06
+-!entry.ACE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 5 0 0 0 0
+-!entry.ACE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "ACE" 1 7 1 "p" 0
+-!entry.ACE.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.ACE.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ACE.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NALA.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.062490
+- "HA" "HP" 0 1 131072 6 1 0.052310
+- "CB" "CT" 0 1 131072 7 6 -0.183710
+- "HB1" "HC" 0 1 131072 8 1 0.085560
+- "HB2" "HC" 0 1 131072 9 1 0.085560
+- "HB3" "HC" 0 1 131072 10 1 0.085560
+- "C" "C" 0 1 131072 11 6 0.670480
+- "O" "O" 0 1 131072 12 8 -0.583250
+-!entry.NALA.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB1" "HC" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NALA.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NALA.unit.childsequence single int
+- 2
+-!entry.NALA.unit.connect array int
+- 0
+- 11
+-!entry.NALA.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 11 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 11 12 1
+-!entry.NALA.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+-!entry.NALA.unit.name single str
+- "NALA"
+-!entry.NALA.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 3.877484 3.115795 2.131197
+- 4.075059 4.623017 1.205786
+- 2.496995 3.801075 1.241379
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NALA.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 11 0 0 0 0
+-!entry.NALA.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NALA" 1 13 1 "p" 0
+-!entry.NALA.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NALA.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NALA.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NARG.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.086660
+- "HA" "HP" 0 1 131072 6 1 0.033450
+- "CB" "CT" 0 1 131072 7 6 0.605740
+- "HB2" "HC" 0 1 131072 8 1 -0.089670
+- "HB3" "HC" 0 1 131072 9 1 -0.111750
+- "CG" "CT" 0 1 131072 10 6 -0.639700
+- "HG2" "HC" 0 1 131072 11 1 0.145340
+- "HG3" "HC" 0 1 131072 12 1 0.145340
+- "CD" "CT" 0 1 131072 13 6 0.616090
+- "HD2" "H1" 0 1 131072 14 1 -0.083600
+- "HD3" "H1" 0 1 131072 15 1 -0.083600
+- "NE" "N2" 0 1 131072 16 7 -0.781830
+- "HE" "H" 0 1 131072 17 1 0.416010
+- "CZ" "CA" 0 1 131072 18 6 1.114550
+- "NH1" "N2" 0 1 131072 19 7 -0.955440
+- "HH11" "H" 0 1 131072 20 1 0.443490
+- "HH12" "H" 0 1 131072 21 1 0.443490
+- "NH2" "N2" 0 1 131072 22 7 -0.955440
+- "HH21" "H" 0 1 131072 23 1 0.443490
+- "HH22" "H" 0 1 131072 24 1 0.443490
+- "C" "C" 0 1 131072 25 6 0.670480
+- "O" "O" 0 1 131072 26 8 -0.583250
+-!entry.NARG.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "H1" 0 -1 0.0
+- "HD3" "H1" 0 -1 0.0
+- "NE" "N2" 0 -1 0.0
+- "HE" "H" 0 -1 0.0
+- "CZ" "CA" 0 -1 0.0
+- "NH1" "N2" 0 -1 0.0
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+- "HH12" "H" 0 -1 0.0
+- "NH2" "N2" 0 -1 0.0
+- "HH21" "H" 0 -1 0.0
+- "HH22" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
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+-!entry.NARG.unit.childsequence single int
+- 2
+-!entry.NARG.unit.connect array int
+- 0
+- 25
+-!entry.NARG.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 25 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
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+- 10 12 1
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+- 16 18 1
+- 18 19 1
+- 18 22 1
+- 19 20 1
+- 19 21 1
+- 22 23 1
+- 22 24 1
+- 25 26 1
+-!entry.NARG.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+- "R" 1 "A" 24
+- "R" 1 "A" 25
+- "R" 1 "A" 26
+-!entry.NARG.unit.name single str
+- "NARG"
+-!entry.NARG.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
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+- 4.274186 5.009602 1.194577
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+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NARG.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 25 0 0 0 0
+-!entry.NARG.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NARG" 1 27 1 "p" 0
+-!entry.NARG.unit.residuesPdbSequenceNumber array int
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+-!entry.NARG.unit.solventcap array dbl
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+-!entry.NARG.unit.velocities table  dbl x  dbl y  dbl z
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+-!entry.NASH.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
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+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 0.084490
+- "HA" "HP" 0 1 131072 6 1 0.002600
+- "CB" "CT" 0 1 131072 7 6 -0.222150
+- "HB2" "HC" 0 1 131072 8 1 0.136250
+- "HB3" "HC" 0 1 131072 9 1 0.136250
+- "CG" "C" 0 1 131072 10 6 0.615590
+- "OD1" "O" 0 1 131072 11 8 -0.553020
+- "OD2" "OH" 0 1 131072 12 8 -0.580780
+- "HD2" "HO" 0 1 131072 13 1 0.443560
+- "C" "C" 0 1 131072 14 6 0.670480
+- "O" "O" 0 1 131072 15 8 -0.583250
+-!entry.NASH.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
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+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C" 0 -1 0.0
+- "OD1" "O" 0 -1 0.0
+- "OD2" "OH" 0 -1 0.0
+- "HD2" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NASH.unit.boundbox array dbl
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+- 0.0
+-!entry.NASH.unit.childsequence single int
+- 2
+-!entry.NASH.unit.connect array int
+- 0
+- 14
+-!entry.NASH.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 14 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 12 13 1
+- 14 15 1
+-!entry.NASH.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+-!entry.NASH.unit.name single str
+- "NASH"
+-!entry.NASH.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
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+- 3.970048 2.845795 -1.311163E-07
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+- 4.275101 5.011380 1.194527
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+- 5.407731 5.091879 1.740667
+- 5.742902 5.987179 1.652920
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NASH.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 14 0 0 0 0
+-!entry.NASH.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NASH" 1 16 1 "p" 0
+-!entry.NASH.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NASH.unit.solventcap array dbl
+- -1.000000
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+- 0.0
+- 0.0
+- 0.0
+-!entry.NASH.unit.velocities table  dbl x  dbl y  dbl z
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+-!entry.NASN.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 0.009080
+- "HA" "HP" 0 1 131072 6 1 0.021090
+- "CB" "CT" 0 1 131072 7 6 -0.279860
+- "HB2" "HC" 0 1 131072 8 1 0.139080
+- "HB3" "HC" 0 1 131072 9 1 0.139080
+- "CG" "C" 0 1 131072 10 6 0.649780
+- "OD1" "O" 0 1 131072 11 8 -0.558030
+- "ND2" "N" 0 1 131072 12 7 -0.826350
+- "HD21" "H" 0 1 131072 13 1 0.384460
+- "HD22" "H" 0 1 131072 14 1 0.384460
+- "C" "C" 0 1 131072 15 6 0.670480
+- "O" "O" 0 1 131072 16 8 -0.583250
+-!entry.NASN.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C" 0 -1 0.0
+- "OD1" "O" 0 -1 0.0
+- "ND2" "N" 0 -1 0.0
+- "HD21" "H" 0 -1 0.0
+- "HD22" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NASN.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NASN.unit.childsequence single int
+- 2
+-!entry.NASN.unit.connect array int
+- 0
+- 15
+-!entry.NASN.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 15 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 12 13 1
+- 12 14 1
+- 15 16 1
+-!entry.NASN.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+-!entry.NASN.unit.name single str
+- "NASN"
+-!entry.NASN.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.253700 5.017112 1.232144
+- 5.005299 5.340406 0.315072
+- 3.984885 5.817909 2.265917
+- 4.408015 6.733702 2.314743
+- 3.359611 5.504297 2.994464
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NASN.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 15 0 0 0 0
+-!entry.NASN.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NASN" 1 17 1 "p" 0
+-!entry.NASN.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NASN.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NASN.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+-!entry.NASP.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.021580
+- "HA" "HP" 0 1 131072 6 1 -0.015560
+- "CB" "CT" 0 1 131072 7 6 -0.319940
+- "HB2" "HC" 0 1 131072 8 1 0.089360
+- "HB3" "HC" 0 1 131072 9 1 0.089360
+- "CG" "C" 0 1 131072 10 6 0.883310
+- "OD1" "O2" 0 1 131072 11 8 -0.821080
+- "OD2" "O2" 0 1 131072 12 8 -0.821080
+- "C" "C" 0 1 131072 13 6 0.670480
+- "O" "O" 0 1 131072 14 8 -0.583250
+-!entry.NASP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C" 0 -1 0.0
+- "OD1" "O2" 0 -1 0.0
+- "OD2" "O2" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NASP.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NASP.unit.childsequence single int
+- 2
+-!entry.NASP.unit.connect array int
+- 0
+- 13
+-!entry.NASP.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 13 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 13 14 1
+-!entry.NASP.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+-!entry.NASP.unit.name single str
+- "NASP"
+-!entry.NASP.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.275101 5.011380 1.194527
+- 3.669108 5.954940 0.620011
+- 5.407731 5.091879 1.740667
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NASP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 13 0 0 0 0
+-!entry.NASP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NASP" 1 15 1 "p" 0
+-!entry.NASP.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NASP.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NASP.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+-!entry.NCYM.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.141590
+- "HA" "HP" 0 1 131072 6 1 0.070220
+- "CB" "CT" 0 1 131072 7 6 0.112010
+- "HB2" "H1" 0 1 131072 8 1 -0.023100
+- "HB3" "H1" 0 1 131072 9 1 -0.023100
+- "SG" "SH" 0 1 131072 10 16 -0.931650
+- "C" "C" 0 1 131072 11 6 0.670480
+- "O" "O" 0 1 131072 12 8 -0.583250
+-!entry.NCYM.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "SG" "SH" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NCYM.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NCYM.unit.childsequence single int
+- 2
+-!entry.NCYM.unit.connect array int
+- 0
+- 11
+-!entry.NCYM.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 11 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 11 12 1
+-!entry.NCYM.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+-!entry.NCYM.unit.name single str
+- "NCYM"
+-!entry.NCYM.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.309573 5.303523 1.366036
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NCYM.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 11 0 0 0 0
+-!entry.NCYM.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NCYM" 1 13 1 "p" 0
+-!entry.NCYM.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NCYM.unit.solventcap array dbl
+- -1.000000
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+- 0.0
+- 0.0
+- 0.0
+-!entry.NCYM.unit.velocities table  dbl x  dbl y  dbl z
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+-!entry.NCYS.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.008690
+- "HA" "HP" 0 1 131072 6 1 0.055730
+- "CB" "CT" 0 1 131072 7 6 -0.028460
+- "HB2" "H1" 0 1 131072 8 1 0.068320
+- "HB3" "H1" 0 1 131072 9 1 0.068320
+- "SG" "SH" 0 1 131072 10 16 -0.250480
+- "HG" "HS" 0 1 131072 11 1 0.158050
+- "C" "C" 0 1 131072 12 6 0.670480
+- "O" "O" 0 1 131072 13 8 -0.583250
+-!entry.NCYS.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "SG" "SH" 0 -1 0.0
+- "HG" "HS" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NCYS.unit.boundbox array dbl
+- -1.000000
+- 0.0
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+- 0.0
+-!entry.NCYS.unit.childsequence single int
+- 2
+-!entry.NCYS.unit.connect array int
+- 0
+- 12
+-!entry.NCYS.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 12 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 12 13 1
+-!entry.NCYS.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+-!entry.NCYS.unit.name single str
+- "NCYS"
+-!entry.NCYS.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.309573 5.303523 1.366036
+- 3.725392 5.622018 2.517640
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NCYS.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 12 0 0 0 0
+-!entry.NCYS.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NCYS" 1 14 1 "p" 0
+-!entry.NCYS.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NCYS.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NCYS.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+-!entry.NCYX.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.016590
+- "HA" "HP" 0 1 131072 6 1 0.026230
+- "CB" "CT" 0 1 131072 7 6 -0.036490
+- "HB2" "H1" 0 1 131072 8 1 0.084950
+- "HB3" "H1" 0 1 131072 9 1 0.084950
+- "SG" "S" 0 1 131072 10 16 -0.080260
+- "C" "C" 0 1 131072 11 6 0.670480
+- "O" "O" 0 1 131072 12 8 -0.583250
+-!entry.NCYX.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "SG" "S" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NCYX.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NCYX.unit.childsequence single int
+- 2
+-!entry.NCYX.unit.connect array int
+- 0
+- 11
+-!entry.NCYX.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 11 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 11 12 1
+-!entry.NCYX.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+-!entry.NCYX.unit.name single str
+- "NCYX"
+-!entry.NCYX.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
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+- 4.309573 5.303523 1.366036
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NCYX.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 11 10 0 0 0
+-!entry.NCYX.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NCYX" 1 13 1 "p" 0
+-!entry.NCYX.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NCYX.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NCYX.unit.velocities table  dbl x  dbl y  dbl z
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+- 0.0 0.0 0.0
+-!entry.NGLH.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.058830
+- "HA" "HP" 0 1 131072 6 1 0.038110
+- "CB" "CT" 0 1 131072 7 6 0.146800
+- "HB2" "HC" 0 1 131072 8 1 0.015120
+- "HB3" "HC" 0 1 131072 9 1 0.015120
+- "CG" "CT" 0 1 131072 10 6 -0.424760
+- "HG2" "HC" 0 1 131072 11 1 0.200810
+- "HG3" "HC" 0 1 131072 12 1 0.200810
+- "CD" "C" 0 1 131072 13 6 0.647590
+- "OE1" "O" 0 1 131072 14 8 -0.569530
+- "OE2" "OH" 0 1 131072 15 8 -0.601150
+- "HE2" "HO" 0 1 131072 16 1 0.452700
+- "C" "C" 0 1 131072 17 6 0.670480
+- "O" "O" 0 1 131072 18 8 -0.583250
+-!entry.NGLH.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "C" 0 -1 0.0
+- "OE1" "O" 0 -1 0.0
+- "OE2" "OH" 0 -1 0.0
+- "HE2" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NGLH.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NGLH.unit.childsequence single int
+- 2
+-!entry.NGLH.unit.connect array int
+- 0
+- 17
+-!entry.NGLH.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 17 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 10 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+- 17 18 1
+-!entry.NGLH.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+-!entry.NGLH.unit.name single str
+- "NGLH"
+-!entry.NGLH.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.267328 4.996267 1.194946
+- 5.347413 4.849843 1.186158
+- 3.966923 5.535124 0.296342
+- 3.873732 5.805369 2.428706
+- 4.594590 5.679012 3.454376
+- 2.855965 6.542070 2.333721
+- 2.710526 6.996624 3.166684
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NGLH.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 17 0 0 0 0
+-!entry.NGLH.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NGLH" 1 19 1 "p" 0
+-!entry.NGLH.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NGLH.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NGLH.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NGLN.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.176770
+- "HA" "HP" 0 1 131072 6 1 0.074450
+- "CB" "CT" 0 1 131072 7 6 0.367300
+- "HB2" "HC" 0 1 131072 8 1 -0.042440
+- "HB3" "HC" 0 1 131072 9 1 -0.042440
+- "CG" "CT" 0 1 131072 10 6 -0.651590
+- "HG2" "HC" 0 1 131072 11 1 0.230560
+- "HG3" "HC" 0 1 131072 12 1 0.230560
+- "CD" "C" 0 1 131072 13 6 0.855380
+- "OE1" "O" 0 1 131072 14 8 -0.671160
+- "NE2" "N" 0 1 131072 15 7 -0.907460
+- "HE21" "H" 0 1 131072 16 1 0.398200
+- "HE22" "H" 0 1 131072 17 1 0.398200
+- "C" "C" 0 1 131072 18 6 0.670480
+- "O" "O" 0 1 131072 19 8 -0.583250
+-!entry.NGLN.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "C" 0 -1 0.0
+- "OE1" "O" 0 -1 0.0
+- "NE2" "N" 0 -1 0.0
+- "HE21" "H" 0 -1 0.0
+- "HE22" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NGLN.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NGLN.unit.childsequence single int
+- 2
+-!entry.NGLN.unit.connect array int
+- 0
+- 18
+-!entry.NGLN.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 18 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 10 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+- 15 17 1
+- 18 19 1
+-!entry.NGLN.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+-!entry.NGLN.unit.name single str
+- "NGLN"
+-!entry.NGLN.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.906976 5.848443 2.410302
+- 3.138962 5.408349 3.262893
+- 4.458856 7.061523 2.488333
+- 4.248434 7.659045 3.274966
+- 5.084281 7.376210 1.760379
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NGLN.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 18 0 0 0 0
+-!entry.NGLN.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NGLN" 1 20 1 "p" 0
+-!entry.NGLN.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NGLN.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NGLN.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NGLU.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.277630
+- "HA" "HP" 0 1 131072 6 1 0.115460
+- "CB" "CT" 0 1 131072 7 6 0.687660
+- "HB2" "HC" 0 1 131072 8 1 -0.198680
+- "HB3" "HC" 0 1 131072 9 1 -0.198680
+- "CG" "CT" 0 1 131072 10 6 -0.615270
+- "HG2" "HC" 0 1 131072 11 1 0.173380
+- "HG3" "HC" 0 1 131072 12 1 0.173380
+- "CD" "C" 0 1 131072 13 6 0.808370
+- "OE1" "O2" 0 1 131072 14 8 -0.802600
+- "OE2" "O2" 0 1 131072 15 8 -0.802600
+- "C" "C" 0 1 131072 16 6 0.670480
+- "O" "O" 0 1 131072 17 8 -0.583250
+-!entry.NGLU.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
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+- "HG3" "HC" 0 -1 0.0
+- "CD" "C" 0 -1 0.0
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+- "C" "C" 0 -1 0.0
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+- 16
+-!entry.NGLU.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
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+- 7 8 1
+- 7 9 1
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+- 13 15 1
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+-!entry.NGLU.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
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+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
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+- "R" 1 "A" 8
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+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+-!entry.NGLU.unit.name single str
+- "NGLU"
+-!entry.NGLU.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
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+- 3.970048 2.845795 -1.311163E-07
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+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NGLU.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 16 0 0 0 0
+-!entry.NGLU.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NGLU" 1 18 1 "p" 0
+-!entry.NGLU.unit.residuesPdbSequenceNumber array int
+- 0
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+-!entry.NGLY.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
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+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
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+- "C" "C" 0 1 131072 8 6 0.670480
+- "O" "O" 0 1 131072 9 8 -0.583250
+-!entry.NGLY.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
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+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA2" "HP" 0 -1 0.0
+- "HA3" "HP" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NGLY.unit.boundbox array dbl
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+- 2
+-!entry.NGLY.unit.connect array int
+- 0
+- 8
+-!entry.NGLY.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+-!entry.NGLY.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+-!entry.NGLY.unit.name single str
+- "NGLY"
+-!entry.NGLY.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
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+- 3.970048 2.845795 -1.311163E-07
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+- 3.671668 3.400125 0.889824
+- 5.483710 2.686702 -4.438857E-06
+- 5.993369 1.568360 -8.469843E-06
+-!entry.NGLY.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 8 0 0 0 0
+-!entry.NGLY.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NGLY" 1 10 1 "p" 0
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+-!entry.NHID.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
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+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.018360
+- "HA" "HP" 0 1 131072 6 1 0.005320
+- "CB" "CT" 0 1 131072 7 6 -0.207970
+- "HB2" "HC" 0 1 131072 8 1 0.122530
+- "HB3" "HC" 0 1 131072 9 1 0.122530
+- "CG" "CC" 0 1 131072 10 6 0.205880
+- "ND1" "NA" 0 1 131072 11 7 -0.380080
+- "HD1" "H" 0 1 131072 12 1 0.357430
+- "CE1" "CR" 0 1 131072 13 6 0.262300
+- "HE1" "H5" 0 1 131072 14 1 0.052860
+- "NE2" "NB" 0 1 131072 15 7 -0.525490
+- "CD2" "CV" 0 1 131072 16 6 -0.029750
+- "HD2" "H4" 0 1 131072 17 1 0.095590
+- "C" "C" 0 1 131072 18 6 0.670480
+- "O" "O" 0 1 131072 19 8 -0.583250
+-!entry.NHID.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
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+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
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+- "HD2" "H4" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NHID.unit.boundbox array dbl
+- -1.000000
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+- 2
+-!entry.NHID.unit.connect array int
+- 0
+- 18
+-!entry.NHID.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 18 1
+- 7 8 1
+- 7 9 1
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+- 10 16 1
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+- 11 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+- 16 17 1
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+-!entry.NHID.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
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+- "R" 1 "A" 3
+- "R" 1 "A" 4
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+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
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+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+-!entry.NHID.unit.name single str
+- "NHID"
+-!entry.NHID.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
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+- 3.877484 3.115795 2.131197
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+- 3.339725 5.691913 3.169805
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+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NHID.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 18 0 0 0 0
+-!entry.NHID.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NHID" 1 20 1 "p" 0
+-!entry.NHID.unit.residuesPdbSequenceNumber array int
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+-!entry.NHID.unit.velocities table  dbl x  dbl y  dbl z
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+-!entry.NHIE.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.035930
+- "HA" "HP" 0 1 131072 6 1 0.022090
+- "CB" "CT" 0 1 131072 7 6 -0.326150
+- "HB2" "HC" 0 1 131072 8 1 0.147760
+- "HB3" "HC" 0 1 131072 9 1 0.147760
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+- "ND1" "NB" 0 1 131072 11 7 -0.678510
+- "CE1" "CR" 0 1 131072 12 6 0.312370
+- "HE1" "H5" 0 1 131072 13 1 0.042060
+- "NE2" "NA" 0 1 131072 14 7 -0.318040
+- "HE2" "H" 0 1 131072 15 1 0.341000
+- "CD2" "CW" 0 1 131072 16 6 -0.217930
+- "HD2" "H4" 0 1 131072 17 1 0.159020
+- "C" "C" 0 1 131072 18 6 0.670480
+- "O" "O" 0 1 131072 19 8 -0.583250
+-!entry.NHIE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
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+- "CA" "CT" 0 -1 0.0
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+- "HD2" "H4" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NHIE.unit.boundbox array dbl
+- -1.000000
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+- 0.0
+-!entry.NHIE.unit.childsequence single int
+- 2
+-!entry.NHIE.unit.connect array int
+- 0
+- 18
+-!entry.NHIE.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 18 1
+- 7 8 1
+- 7 9 1
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+- 10 11 1
+- 10 16 1
+- 11 12 1
+- 12 13 1
+- 12 14 1
+- 14 15 1
+- 14 16 1
+- 16 17 1
+- 18 19 1
+-!entry.NHIE.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
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+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+-!entry.NHIE.unit.name single str
+- "NHIE"
+-!entry.NHIE.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.942782 5.885086 2.382972
+- 4.624274 6.997642 2.182500
+- 4.563048 7.811875 2.904563
+- 5.294011 6.891451 1.061663
+- 5.896297 7.605085 0.676854
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+- 5.537741 5.417846 -0.451343
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NHIE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 18 0 0 0 0
+-!entry.NHIE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NHIE" 1 20 1 "p" 0
+-!entry.NHIE.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NHIE.unit.solventcap array dbl
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+-!entry.NHIE.unit.velocities table  dbl x  dbl y  dbl z
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+-!entry.NHIP.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 0.119410
+- "HA" "HP" 0 1 131072 6 1 -0.053970
+- "CB" "CT" 0 1 131072 7 6 -0.059690
+- "HB2" "HC" 0 1 131072 8 1 0.073300
+- "HB3" "HC" 0 1 131072 9 1 0.073300
+- "CG" "CC" 0 1 131072 10 6 0.259530
+- "ND1" "NA" 0 1 131072 11 7 -0.115370
+- "HD1" "H" 0 1 131072 12 1 0.355750
+- "CE1" "CR" 0 1 131072 13 6 -0.085390
+- "HE1" "H5" 0 1 131072 14 1 0.198640
+- "NE2" "NA" 0 1 131072 15 7 0.055360
+- "HE2" "H" 0 1 131072 16 1 0.293500
+- "CD2" "CW" 0 1 131072 17 6 -0.207090
+- "HD2" "H4" 0 1 131072 18 1 0.155510
+- "C" "C" 0 1 131072 19 6 0.670480
+- "O" "O" 0 1 131072 20 8 -0.583250
+-!entry.NHIP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
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+- "HB3" "HC" 0 -1 0.0
+- "CG" "CC" 0 -1 0.0
+- "ND1" "NA" 0 -1 0.0
+- "HD1" "H" 0 -1 0.0
+- "CE1" "CR" 0 -1 0.0
+- "HE1" "H5" 0 -1 0.0
+- "NE2" "NA" 0 -1 0.0
+- "HE2" "H" 0 -1 0.0
+- "CD2" "CW" 0 -1 0.0
+- "HD2" "H4" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NHIP.unit.boundbox array dbl
+- -1.000000
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+-!entry.NHIP.unit.childsequence single int
+- 2
+-!entry.NHIP.unit.connect array int
+- 0
+- 19
+-!entry.NHIP.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 19 1
+- 7 8 1
+- 7 9 1
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+- 11 12 1
+- 11 13 1
+- 13 14 1
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+- 15 16 1
+- 15 17 1
+- 17 18 1
+- 19 20 1
+-!entry.NHIP.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+-!entry.NHIP.unit.name single str
+- "NHIP"
+-!entry.NHIP.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.942782 5.885086 2.382972
+- 3.339725 5.691913 3.169805
+- 4.624274 6.997642 2.182500
+- 4.563048 7.811875 2.904563
+- 5.294011 6.891451 1.061663
+- 5.896297 7.605085 0.676854
+- 5.058974 5.678868 0.492453
+- 5.537741 5.417846 -0.451343
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NHIP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 19 0 0 0 0
+-!entry.NHIP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NHIP" 1 21 1 "p" 0
+-!entry.NHIP.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NHIP.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NHIP.unit.velocities table  dbl x  dbl y  dbl z
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+-!entry.NILE.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.229690
+- "HA" "HP" 0 1 131072 6 1 0.080520
+- "CB" "CT" 0 1 131072 7 6 0.455630
+- "HB" "HC" 0 1 131072 8 1 -0.113680
+- "CG2" "CT" 0 1 131072 9 6 -0.498950
+- "HG21" "HC" 0 1 131072 10 1 0.129740
+- "HG22" "HC" 0 1 131072 11 1 0.129740
+- "HG23" "HC" 0 1 131072 12 1 0.129740
+- "CG1" "CT" 0 1 131072 13 6 -0.144720
+- "HG12" "HC" 0 1 131072 14 1 0.066780
+- "HG13" "HC" 0 1 131072 15 1 0.066780
+- "CD1" "CT" 0 1 131072 16 6 -0.134770
+- "HD11" "HC" 0 1 131072 17 1 0.041890
+- "HD12" "HC" 0 1 131072 18 1 0.041890
+- "HD13" "HC" 0 1 131072 19 1 0.041890
+- "C" "C" 0 1 131072 20 6 0.670480
+- "O" "O" 0 1 131072 21 8 -0.583250
+-!entry.NILE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB" "HC" 0 -1 0.0
+- "CG2" "CT" 0 -1 0.0
+- "HG21" "HC" 0 -1 0.0
+- "HG22" "HC" 0 -1 0.0
+- "HG23" "HC" 0 -1 0.0
+- "CG1" "CT" 0 -1 0.0
+- "HG12" "HC" 0 -1 0.0
+- "HG13" "HC" 0 -1 0.0
+- "CD1" "CT" 0 -1 0.0
+- "HD11" "HC" 0 -1 0.0
+- "HD12" "HC" 0 -1 0.0
+- "HD13" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NILE.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NILE.unit.childsequence single int
+- 2
+-!entry.NILE.unit.connect array int
+- 0
+- 20
+-!entry.NILE.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 20 1
+- 7 8 1
+- 7 9 1
+- 7 13 1
+- 9 10 1
+- 9 11 1
+- 9 12 1
+- 13 14 1
+- 13 15 1
+- 13 16 1
+- 16 17 1
+- 16 18 1
+- 16 19 1
+- 20 21 1
+-!entry.NILE.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+-!entry.NILE.unit.name single str
+- "NILE"
+-!entry.NILE.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.552136 3.620733 1.245168
+- 2.470128 3.752486 1.245640
+- 3.970045 2.845728 2.490296
+- 5.052053 2.713974 2.490763
+- 3.671561 3.399208 3.380615
+- 3.485650 1.869275 2.490737
+- 4.230204 4.986694 1.245169
+- 3.931820 5.541027 0.355348
+- 5.312310 4.855746 1.245164
+- 3.812294 5.761632 2.490339
+- 4.110777 5.208104 3.380628
+- 4.296689 6.738085 2.490833
+- 2.730286 5.893383 2.490813
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NILE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 20 0 0 0 0
+-!entry.NILE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NILE" 1 22 1 "p" 0
+-!entry.NILE.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NILE.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NILE.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NLEU.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.048190
+- "HA" "HP" 0 1 131072 6 1 0.009070
+- "CB" "CT" 0 1 131072 7 6 -0.232000
+- "HB2" "HC" 0 1 131072 8 1 0.091230
+- "HB3" "HC" 0 1 131072 9 1 0.091230
+- "CG" "CT" 0 1 131072 10 6 0.595680
+- "HG" "HC" 0 1 131072 11 1 -0.106730
+- "CD1" "CT" 0 1 131072 12 6 -0.811380
+- "HD11" "HC" 0 1 131072 13 1 0.214210
+- "HD12" "HC" 0 1 131072 14 1 0.214210
+- "HD13" "HC" 0 1 131072 15 1 0.214210
+- "CD2" "CT" 0 1 131072 16 6 -0.811380
+- "HD21" "HC" 0 1 131072 17 1 0.214210
+- "HD22" "HC" 0 1 131072 18 1 0.214210
+- "HD23" "HC" 0 1 131072 19 1 0.214210
+- "C" "C" 0 1 131072 20 6 0.670480
+- "O" "O" 0 1 131072 21 8 -0.583250
+-!entry.NLEU.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG" "HC" 0 -1 0.0
+- "CD1" "CT" 0 -1 0.0
+- "HD11" "HC" 0 -1 0.0
+- "HD12" "HC" 0 -1 0.0
+- "HD13" "HC" 0 -1 0.0
+- "CD2" "CT" 0 -1 0.0
+- "HD21" "HC" 0 -1 0.0
+- "HD22" "HC" 0 -1 0.0
+- "HD23" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NLEU.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NLEU.unit.childsequence single int
+- 2
+-!entry.NLEU.unit.connect array int
+- 0
+- 20
+-!entry.NLEU.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 20 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 10 16 1
+- 12 13 1
+- 12 14 1
+- 12 15 1
+- 16 17 1
+- 16 18 1
+- 16 19 1
+- 20 21 1
+-!entry.NLEU.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+-!entry.NLEU.unit.name single str
+- "NLEU"
+-!entry.NLEU.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.853429 5.762895 -0.062857
+- 2.773449 5.910113 -0.054557
+- 4.351513 6.732052 -0.090203
+- 4.134159 5.185704 -0.943846
+- 3.881105 5.817645 2.426721
+- 4.181626 5.279602 3.325774
+- 4.379198 6.786825 2.400363
+- 2.801135 5.964881 2.435959
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NLEU.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 20 0 0 0 0
+-!entry.NLEU.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NLEU" 1 22 1 "p" 0
+-!entry.NLEU.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NLEU.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NLEU.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NLYN.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.095720
+- "HA" "HP" 0 1 131072 6 1 0.049030
+- "CB" "CT" 0 1 131072 7 6 0.079910
+- "HB2" "HC" 0 1 131072 8 1 -0.013700
+- "HB3" "HC" 0 1 131072 9 1 -0.013700
+- "CG" "CT" 0 1 131072 10 6 0.022200
+- "HG2" "HC" 0 1 131072 11 1 0.016820
+- "HG3" "HC" 0 1 131072 12 1 0.016820
+- "CD" "CT" 0 1 131072 13 6 -0.303010
+- "HD2" "HC" 0 1 131072 14 1 0.123310
+- "HD3" "HC" 0 1 131072 15 1 0.123310
+- "CE" "CT" 0 1 131072 16 6 0.555520
+- "HE2" "HP" 0 1 131072 17 1 -0.113930
+- "HE3" "HP" 0 1 131072 18 1 -0.113930
+- "NZ" "NT" 0 1 131072 19 7 -0.979040
+- "HZ2" "H" 0 1 131072 20 1 0.354450
+- "HZ3" "H" 0 1 131072 21 1 0.354450
+- "C" "C" 0 1 131072 22 6 0.670480
+- "O" "O" 0 1 131072 23 8 -0.583250
+-!entry.NLYN.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "HC" 0 -1 0.0
+- "HD3" "HC" 0 -1 0.0
+- "CE" "CT" 0 -1 0.0
+- "HE2" "HP" 0 -1 0.0
+- "HE3" "HP" 0 -1 0.0
+- "NZ" "NT" 0 -1 0.0
+- "HZ2" "H" 0 -1 0.0
+- "HZ3" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NLYN.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NLYN.unit.childsequence single int
+- 2
+-!entry.NLYN.unit.connect array int
+- 0
+- 22
+-!entry.NLYN.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 22 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 10 13 1
+- 13 14 1
+- 13 15 1
+- 13 16 1
+- 16 17 1
+- 16 18 1
+- 16 19 1
+- 19 20 1
+- 19 21 1
+- 22 23 1
+-!entry.NLYN.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+-!entry.NLYN.unit.name single str
+- "NLYN"
+-!entry.NLYN.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.881105 5.817645 2.426721
+- 2.801135 5.964881 2.435959
+- 4.181626 5.279602 3.325774
+- 4.578325 7.173410 2.389153
+- 5.658410 7.026987 2.380363
+- 4.277917 7.712267 1.490550
+- 4.199422 7.952309 3.576860
+- 4.661186 8.850226 3.551979
+- 3.198675 8.088466 3.584971
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NLYN.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 22 0 0 0 0
+-!entry.NLYN.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NLYN" 1 24 1 "p" 0
+-!entry.NLYN.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NLYN.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NLYN.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NLYS.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.109440
+- "HA" "HP" 0 1 131072 6 1 0.074110
+- "CB" "CT" 0 1 131072 7 6 0.027560
+- "HB2" "HC" 0 1 131072 8 1 0.006150
+- "HB3" "HC" 0 1 131072 9 1 0.006150
+- "CG" "CT" 0 1 131072 10 6 -0.012430
+- "HG2" "HC" 0 1 131072 11 1 0.044300
+- "HG3" "HC" 0 1 131072 12 1 0.044300
+- "CD" "CT" 0 1 131072 13 6 -0.229220
+- "HD2" "HC" 0 1 131072 14 1 0.103290
+- "HD3" "HC" 0 1 131072 15 1 0.103290
+- "CE" "CT" 0 1 131072 16 6 0.454620
+- "HE2" "HP" 0 1 131072 17 1 -0.045920
+- "HE3" "HP" 0 1 131072 18 1 -0.045920
+- "NZ" "N3" 0 1 131072 19 7 -0.357710
+- "HZ1" "H" 0 1 131072 20 1 0.333220
+- "HZ2" "H" 0 1 131072 21 1 0.333220
+- "HZ3" "H" 0 1 131072 22 1 0.333220
+- "C" "C" 0 1 131072 23 6 0.670480
+- "O" "O" 0 1 131072 24 8 -0.583250
+-!entry.NLYS.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "HC" 0 -1 0.0
+- "HD3" "HC" 0 -1 0.0
+- "CE" "CT" 0 -1 0.0
+- "HE2" "HP" 0 -1 0.0
+- "HE3" "HP" 0 -1 0.0
+- "NZ" "N3" 0 -1 0.0
+- "HZ1" "H" 0 -1 0.0
+- "HZ2" "H" 0 -1 0.0
+- "HZ3" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NLYS.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NLYS.unit.childsequence single int
+- 2
+-!entry.NLYS.unit.connect array int
+- 0
+- 23
+-!entry.NLYS.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 23 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 10 13 1
+- 13 14 1
+- 13 15 1
+- 13 16 1
+- 16 17 1
+- 16 18 1
+- 16 19 1
+- 19 20 1
+- 19 21 1
+- 19 22 1
+- 23 24 1
+-!entry.NLYS.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+- "R" 1 "A" 24
+-!entry.NLYS.unit.name single str
+- "NLYS"
+-!entry.NLYS.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.881105 5.817645 2.426721
+- 2.801135 5.964881 2.435959
+- 4.181626 5.279602 3.325774
+- 4.578325 7.173410 2.389153
+- 5.658410 7.026987 2.380363
+- 4.277917 7.712267 1.490550
+- 4.199422 7.952309 3.576860
+- 4.478085 7.453366 4.409628
+- 4.661186 8.850226 3.551979
+- 3.198675 8.088466 3.584971
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NLYS.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 23 0 0 0 0
+-!entry.NLYS.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NLYS" 1 25 1 "p" 0
+-!entry.NLYS.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NLYS.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NLYS.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NMET.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.097630
+- "HA" "HP" 0 1 131072 6 1 0.070210
+- "CB" "CT" 0 1 131072 7 6 0.275580
+- "HB2" "HC" 0 1 131072 8 1 -0.049150
+- "HB3" "HC" 0 1 131072 9 1 -0.049150
+- "CG" "CT" 0 1 131072 10 6 -0.318690
+- "HG2" "H1" 0 1 131072 11 1 0.142380
+- "HG3" "H1" 0 1 131072 12 1 0.142380
+- "SD" "S" 0 1 131072 13 16 -0.124640
+- "CE" "CT" 0 1 131072 14 6 -0.228860
+- "HE1" "H1" 0 1 131072 15 1 0.100120
+- "HE2" "H1" 0 1 131072 16 1 0.100120
+- "HE3" "H1" 0 1 131072 17 1 0.100120
+- "C" "C" 0 1 131072 18 6 0.670480
+- "O" "O" 0 1 131072 19 8 -0.583250
+-!entry.NMET.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "H1" 0 -1 0.0
+- "HG3" "H1" 0 -1 0.0
+- "SD" "S" 0 -1 0.0
+- "CE" "CT" 0 -1 0.0
+- "HE1" "H1" 0 -1 0.0
+- "HE2" "H1" 0 -1 0.0
+- "HE3" "H1" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NMET.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NMET.unit.childsequence single int
+- 2
+-!entry.NMET.unit.connect array int
+- 0
+- 18
+-!entry.NMET.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 18 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 10 13 1
+- 13 14 1
+- 14 15 1
+- 14 16 1
+- 14 17 1
+- 18 19 1
+-!entry.NMET.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+-!entry.NMET.unit.name single str
+- "NMET"
+-!entry.NMET.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.817309 5.981266 2.651708
+- 4.753212 7.463128 2.340949
+- 4.433582 7.904044 1.396741
+- 4.585907 8.175299 3.148985
+- 5.814074 7.218763 2.286554
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NMET.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 18 0 0 0 0
+-!entry.NMET.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NMET" 1 20 1 "p" 0
+-!entry.NMET.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NMET.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NMET.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NPHE.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.033820
+- "HA" "HP" 0 1 131072 6 1 0.035950
+- "CB" "CT" 0 1 131072 7 6 -0.264720
+- "HB2" "HC" 0 1 131072 8 1 0.129600
+- "HB3" "HC" 0 1 131072 9 1 0.129600
+- "CG" "CA" 0 1 131072 10 6 0.233490
+- "CD1" "CA" 0 1 131072 11 6 -0.246420
+- "HD1" "HA" 0 1 131072 12 1 0.151840
+- "CE1" "CA" 0 1 131072 13 6 -0.076860
+- "HE1" "HA" 0 1 131072 14 1 0.108390
+- "CZ" "CA" 0 1 131072 15 6 -0.134740
+- "HZ" "HA" 0 1 131072 16 1 0.093530
+- "CE2" "CA" 0 1 131072 17 6 -0.076860
+- "HE2" "HA" 0 1 131072 18 1 0.108390
+- "CD2" "CA" 0 1 131072 19 6 -0.246420
+- "HD2" "HA" 0 1 131072 20 1 0.151840
+- "C" "C" 0 1 131072 21 6 0.670480
+- "O" "O" 0 1 131072 22 8 -0.583250
+-!entry.NPHE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CA" 0 -1 0.0
+- "CD1" "CA" 0 -1 0.0
+- "HD1" "HA" 0 -1 0.0
+- "CE1" "CA" 0 -1 0.0
+- "HE1" "HA" 0 -1 0.0
+- "CZ" "CA" 0 -1 0.0
+- "HZ" "HA" 0 -1 0.0
+- "CE2" "CA" 0 -1 0.0
+- "HE2" "HA" 0 -1 0.0
+- "CD2" "CA" 0 -1 0.0
+- "HD2" "HA" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NPHE.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NPHE.unit.childsequence single int
+- 2
+-!entry.NPHE.unit.connect array int
+- 0
+- 21
+-!entry.NPHE.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 21 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 19 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+- 15 17 1
+- 17 18 1
+- 17 19 1
+- 19 20 1
+- 21 22 1
+-!entry.NPHE.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+-!entry.NPHE.unit.name single str
+- "NPHE"
+-!entry.NPHE.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.911613 5.857250 2.409890
+- 3.236123 5.513843 3.193398
+- 4.490014 7.129513 2.492354
+- 4.264853 7.776651 3.340066
+- 5.357616 7.570591 1.486016
+- 5.807943 8.561138 1.550220
+- 5.646818 6.739407 0.397211
+- 6.322309 7.082817 -0.386295
+- 5.068419 5.467143 0.314744
+- 5.293584 4.820007 -0.532968
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NPHE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 21 0 0 0 0
+-!entry.NPHE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NPHE" 1 23 1 "p" 0
+-!entry.NPHE.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NPHE.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NPHE.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NPRO.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 -0.138570
+- "H2" "H" 0 1 131072 2 1 0.257280
+- "H3" "H" 0 1 131072 3 1 0.257280
+- "CD" "CT" 0 1 131072 4 6 0.227570
+- "HD2" "HP" 0 1 131072 5 1 0.017160
+- "HD3" "HP" 0 1 131072 6 1 0.017150
+- "CG" "CT" 0 1 131072 7 6 -0.073460
+- "HG2" "HC" 0 1 131072 8 1 0.038960
+- "HG3" "HC" 0 1 131072 9 1 0.038960
+- "CB" "CT" 0 1 131072 10 6 0.189500
+- "HB2" "HC" 0 1 131072 11 1 -0.029230
+- "HB3" "HC" 0 1 131072 12 1 -0.029230
+- "CA" "CT" 0 1 131072 13 6 0.104090
+- "HA" "HP" 0 1 131072 14 1 0.035310
+- "C" "C" 0 1 131072 15 6 0.670480
+- "O" "O" 0 1 131072 16 8 -0.583250
+-!entry.NPRO.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "HP" 0 -1 0.0
+- "HD3" "HP" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NPRO.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NPRO.unit.childsequence single int
+- 2
+-!entry.NPRO.unit.connect array int
+- 0
+- 15
+-!entry.NPRO.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 13 1
+- 4 5 1
+- 4 6 1
+- 4 7 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 10 12 1
+- 10 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+-!entry.NPRO.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+-!entry.NPRO.unit.name single str
+- "NPRO"
+-!entry.NPRO.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 4.293514 0.460336 0.080119
+- 4.408169 0.002209 -0.902263
+- 3.942023 -0.287867 0.790574
+- 5.543321 1.147470 0.544693
+- 6.406715 0.710627 0.042879
+- 5.648273 1.022228 1.622376
+- 5.375453 2.604421 0.185227
+- 5.977268 2.833902 -0.694123
+- 5.701345 3.225015 1.019947
+- 3.941704 2.857529 -0.104508
+- 3.623882 3.477056 0.734106
+- 3.517842 3.515620 -1.409783
+- 2.762837 2.933549 -2.185412
+-!entry.NPRO.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 15 0 0 0 0
+-!entry.NPRO.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NPRO" 1 17 1 "p" 0
+-!entry.NPRO.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NPRO.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
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+-!entry.NPRO.unit.velocities table  dbl x  dbl y  dbl z
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+-!entry.NSER.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 0.006090
+- "HA" "HP" 0 1 131072 6 1 0.050540
+- "CB" "CT" 0 1 131072 7 6 0.197970
+- "HB2" "H1" 0 1 131072 8 1 0.017960
+- "HB3" "H1" 0 1 131072 9 1 0.017970
+- "OG" "OH" 0 1 131072 10 8 -0.606020
+- "HG" "HO" 0 1 131072 11 1 0.378280
+- "C" "C" 0 1 131072 12 6 0.670480
+- "O" "O" 0 1 131072 13 8 -0.583250
+-!entry.NSER.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "OG" "OH" 0 -1 0.0
+- "HG" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NSER.unit.boundbox array dbl
+- -1.000000
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+- 0.0
+- 0.0
+- 0.0
+-!entry.NSER.unit.childsequence single int
+- 2
+-!entry.NSER.unit.connect array int
+- 0
+- 12
+-!entry.NSER.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 12 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
+- 12 13 1
+-!entry.NSER.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+-!entry.NSER.unit.name single str
+- "NSER"
+-!entry.NSER.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.230753 4.925145 1.196917
+- 3.983305 5.433814 1.972562
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NSER.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 12 0 0 0 0
+-!entry.NSER.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NSER" 1 14 1 "p" 0
+-!entry.NSER.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NSER.unit.solventcap array dbl
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+-!entry.NSER.unit.velocities table  dbl x  dbl y  dbl z
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+-!entry.NTHR.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 0.036230
+- "HA" "HP" 0 1 131072 6 1 0.028680
+- "CB" "CT" 0 1 131072 7 6 0.563540
+- "HB" "H1" 0 1 131072 8 1 -0.161960
+- "CG2" "CT" 0 1 131072 9 6 -0.574400
+- "HG21" "HC" 0 1 131072 10 1 0.154000
+- "HG22" "HC" 0 1 131072 11 1 0.154000
+- "HG23" "HC" 0 1 131072 12 1 0.154000
+- "OG1" "OH" 0 1 131072 13 8 -0.735860
+- "HG1" "HO" 0 1 131072 14 1 0.444560
+- "C" "C" 0 1 131072 15 6 0.670480
+- "O" "O" 0 1 131072 16 8 -0.583250
+-!entry.NTHR.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB" "H1" 0 -1 0.0
+- "CG2" "CT" 0 -1 0.0
+- "HG21" "HC" 0 -1 0.0
+- "HG22" "HC" 0 -1 0.0
+- "HG23" "HC" 0 -1 0.0
+- "OG1" "OH" 0 -1 0.0
+- "HG1" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NTHR.unit.boundbox array dbl
+- -1.000000
+- 0.0
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+- 0.0
+- 0.0
+-!entry.NTHR.unit.childsequence single int
+- 2
+-!entry.NTHR.unit.connect array int
+- 0
+- 15
+-!entry.NTHR.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 15 1
+- 7 8 1
+- 7 9 1
+- 7 13 1
+- 9 10 1
+- 9 11 1
+- 9 12 1
+- 13 14 1
+- 15 16 1
+-!entry.NTHR.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+-!entry.NTHR.unit.name single str
+- "NTHR"
+-!entry.NTHR.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 4.075059 4.623017 1.205786
+- 2.065936 3.859425 1.244383
+- 1.567127 2.890627 1.271209
+- 1.784431 4.436953 2.124903
+- 1.764699 4.397847 0.345796
+- 3.971501 2.947413 2.411212
+- 3.724052 3.456082 3.186857
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NTHR.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 15 0 0 0 0
+-!entry.NTHR.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NTHR" 1 17 1 "p" 0
+-!entry.NTHR.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NTHR.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NTHR.unit.velocities table  dbl x  dbl y  dbl z
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+-!entry.NTRP.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.064400
+- "HA" "HP" 0 1 131072 6 1 0.060910
+- "CB" "CT" 0 1 131072 7 6 0.072380
+- "HB2" "HC" 0 1 131072 8 1 0.023340
+- "HB3" "HC" 0 1 131072 9 1 0.023340
+- "CG" "C*" 0 1 131072 10 6 -0.302580
+- "CD1" "CW" 0 1 131072 11 6 0.030860
+- "HD1" "H4" 0 1 131072 12 1 0.139310
+- "NE1" "NA" 0 1 131072 13 7 -0.480170
+- "HE1" "H" 0 1 131072 14 1 0.392790
+- "CE2" "CN" 0 1 131072 15 6 0.192760
+- "CZ2" "CA" 0 1 131072 16 6 -0.261010
+- "HZ2" "HA" 0 1 131072 17 1 0.183580
+- "CH2" "CA" 0 1 131072 18 6 -0.180740
+- "HH2" "HA" 0 1 131072 19 1 0.106860
+- "CZ3" "CA" 0 1 131072 20 6 -0.044730
+- "HZ3" "HA" 0 1 131072 21 1 0.086480
+- "CE3" "CA" 0 1 131072 22 6 -0.427910
+- "HE3" "HA" 0 1 131072 23 1 0.225690
+- "CD2" "CB" 0 1 131072 24 6 0.286030
+- "C" "C" 0 1 131072 25 6 0.670480
+- "O" "O" 0 1 131072 26 8 -0.583250
+-!entry.NTRP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C*" 0 -1 0.0
+- "CD1" "CW" 0 -1 0.0
+- "HD1" "H4" 0 -1 0.0
+- "NE1" "NA" 0 -1 0.0
+- "HE1" "H" 0 -1 0.0
+- "CE2" "CN" 0 -1 0.0
+- "CZ2" "CA" 0 -1 0.0
+- "HZ2" "HA" 0 -1 0.0
+- "CH2" "CA" 0 -1 0.0
+- "HH2" "HA" 0 -1 0.0
+- "CZ3" "CA" 0 -1 0.0
+- "HZ3" "HA" 0 -1 0.0
+- "CE3" "CA" 0 -1 0.0
+- "HE3" "HA" 0 -1 0.0
+- "CD2" "CB" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NTRP.unit.boundbox array dbl
+- -1.000000
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+- 0.0
+-!entry.NTRP.unit.childsequence single int
+- 2
+-!entry.NTRP.unit.connect array int
+- 0
+- 25
+-!entry.NTRP.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 25 1
+- 7 8 1
+- 7 9 1
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+- 16 18 1
+- 18 19 1
+- 18 20 1
+- 20 21 1
+- 20 22 1
+- 22 23 1
+- 22 24 1
+- 25 26 1
+-!entry.NTRP.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+- "R" 1 "A" 24
+- "R" 1 "A" 25
+- "R" 1 "A" 26
+-!entry.NTRP.unit.name single str
+- "NTRP"
+-!entry.NTRP.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 4.023453 5.931084 2.293240
+- 3.368841 5.705466 3.135071
+- 4.811943 7.073555 1.949808
+- 4.882921 7.922010 2.493118
+- 5.427347 6.842060 0.816764
+- 6.297161 7.689052 0.119605
+- 6.531230 8.676649 0.517050
+- 6.814091 7.187011 -1.069023
+- 7.498074 7.791857 -1.664362
+- 6.482659 5.953119 -1.505101
+- 6.897660 5.575648 -2.439654
+- 5.604041 5.117355 -0.785636
+- 5.358720 4.126570 -1.168080
+- 5.083390 5.623004 0.411545
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NTRP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 25 0 0 0 0
+-!entry.NTRP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NTRP" 1 27 1 "p" 0
+-!entry.NTRP.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NTRP.unit.solventcap array dbl
+- -1.000000
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+- 0.0
+- 0.0
+-!entry.NTRP.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NTYR.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.117360
+- "HA" "HP" 0 1 131072 6 1 0.085560
+- "CB" "CT" 0 1 131072 7 6 -0.110270
+- "HB2" "HC" 0 1 131072 8 1 0.083860
+- "HB3" "HC" 0 1 131072 9 1 0.083860
+- "CG" "CA" 0 1 131072 10 6 0.037350
+- "CD1" "CA" 0 1 131072 11 6 -0.143640
+- "HD1" "HA" 0 1 131072 12 1 0.146300
+- "CE1" "CA" 0 1 131072 13 6 -0.334390
+- "HE1" "HA" 0 1 131072 14 1 0.190770
+- "CZ" "CA" 0 1 131072 15 6 0.444500
+- "OH" "OH" 0 1 131072 16 8 -0.546480
+- "HH" "HO" 0 1 131072 17 1 0.383690
+- "CE2" "CA" 0 1 131072 18 6 -0.334390
+- "HE2" "HA" 0 1 131072 19 1 0.190770
+- "CD2" "CA" 0 1 131072 20 6 -0.143640
+- "HD2" "HA" 0 1 131072 21 1 0.146300
+- "C" "C" 0 1 131072 22 6 0.670480
+- "O" "O" 0 1 131072 23 8 -0.583250
+-!entry.NTYR.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CA" 0 -1 0.0
+- "CD1" "CA" 0 -1 0.0
+- "HD1" "HA" 0 -1 0.0
+- "CE1" "CA" 0 -1 0.0
+- "HE1" "HA" 0 -1 0.0
+- "CZ" "CA" 0 -1 0.0
+- "OH" "OH" 0 -1 0.0
+- "HH" "HO" 0 -1 0.0
+- "CE2" "CA" 0 -1 0.0
+- "HE2" "HA" 0 -1 0.0
+- "CD2" "CA" 0 -1 0.0
+- "HD2" "HA" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NTYR.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NTYR.unit.childsequence single int
+- 2
+-!entry.NTYR.unit.connect array int
+- 0
+- 22
+-!entry.NTYR.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 22 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 10 11 1
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+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+- 15 18 1
+- 16 17 1
+- 18 19 1
+- 18 20 1
+- 20 21 1
+- 22 23 1
+-!entry.NTYR.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+-!entry.NTYR.unit.name single str
+- "NTYR"
+-!entry.NTYR.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.267328 4.996267 1.194946
+- 4.059927 5.918911 2.227280
+- 3.400108 5.668218 3.057877
+- 4.699998 7.163547 2.192791
+- 4.538522 7.881891 2.996538
+- 5.547471 7.485542 1.125970
+- 6.169255 8.694617 1.092468
+- 5.956327 9.246984 1.848214
+- 5.754875 6.562900 0.093635
+- 6.414694 6.813595 -0.736962
+- 5.114806 5.318263 0.128119
+- 5.276286 4.599920 -0.675627
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NTYR.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 22 0 0 0 0
+-!entry.NTYR.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NTYR" 1 24 1 "p" 0
+-!entry.NTYR.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NTYR.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NTYR.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.NVAL.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N3" 0 1 131072 1 7 0.351680
+- "H1" "H" 0 1 131072 2 1 0.166100
+- "H2" "H" 0 1 131072 3 1 0.166100
+- "H3" "H" 0 1 131072 4 1 0.166100
+- "CA" "CT" 0 1 131072 5 6 -0.131460
+- "HA" "HP" 0 1 131072 6 1 0.055960
+- "CB" "CT" 0 1 131072 7 6 0.600860
+- "HB" "HC" 0 1 131072 8 1 -0.088610
+- "CG1" "CT" 0 1 131072 9 6 -0.789890
+- "HG11" "HC" 0 1 131072 10 1 0.200970
+- "HG12" "HC" 0 1 131072 11 1 0.200970
+- "HG13" "HC" 0 1 131072 12 1 0.200970
+- "CG2" "CT" 0 1 131072 13 6 -0.789890
+- "HG21" "HC" 0 1 131072 14 1 0.200970
+- "HG22" "HC" 0 1 131072 15 1 0.200970
+- "HG23" "HC" 0 1 131072 16 1 0.200970
+- "C" "C" 0 1 131072 17 6 0.670480
+- "O" "O" 0 1 131072 18 8 -0.583250
+-!entry.NVAL.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N3" 0 -1 0.0
+- "H1" "H" 0 -1 0.0
+- "H2" "H" 0 -1 0.0
+- "H3" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "HP" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB" "HC" 0 -1 0.0
+- "CG1" "CT" 0 -1 0.0
+- "HG11" "HC" 0 -1 0.0
+- "HG12" "HC" 0 -1 0.0
+- "HG13" "HC" 0 -1 0.0
+- "CG2" "CT" 0 -1 0.0
+- "HG21" "HC" 0 -1 0.0
+- "HG22" "HC" 0 -1 0.0
+- "HG23" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.NVAL.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NVAL.unit.childsequence single int
+- 2
+-!entry.NVAL.unit.connect array int
+- 0
+- 17
+-!entry.NVAL.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 1 4 1
+- 1 5 1
+- 5 6 1
+- 5 7 1
+- 5 17 1
+- 7 8 1
+- 7 9 1
+- 7 13 1
+- 9 10 1
+- 9 11 1
+- 9 12 1
+- 13 14 1
+- 13 15 1
+- 13 16 1
+- 17 18 1
+-!entry.NVAL.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+-!entry.NVAL.unit.name single str
+- "NVAL"
+-!entry.NVAL.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 4.046154 0.839991 -2.855245E-06
+- 2.823094 1.499508 -0.874687
+- 2.823097 1.499507 0.874685
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.997712 2.900483 2.489542
+- 5.077693 2.753265 2.481244
+- 3.716972 3.477628 3.370558
+- 3.499630 1.931323 2.516834
+- 4.274186 5.009602 1.194577
+- 3.973781 5.548460 0.295972
+- 3.993559 5.587585 2.075079
+- 5.354271 4.863178 1.185788
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.NVAL.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 0 17 0 0 0 0
+-!entry.NVAL.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "NVAL" 1 19 1 "p" 0
+-!entry.NVAL.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.NVAL.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.NVAL.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+diff --git a/dat/leap/lib/aminopol12.lib b/dat/leap/lib/aminopol12.lib
+deleted file mode 100644
+index ed9039d..0000000
+--- a/dat/leap/lib/aminopol12.lib
++++ /dev/null
+@@ -1,3521 +0,0 @@
+-!!index array str
+- "ALA"
+- "ARG"
+- "ASH"
+- "ASN"
+- "ASP"
+- "CIM"
+- "CIP"
+- "CYM"
+- "CYS"
+- "CYX"
+- "GLH"
+- "GLN"
+- "GLU"
+- "GLY"
+- "HID"
+- "HIE"
+- "HIP"
+- "ILE"
+- "LEU"
+- "LYN"
+- "LYS"
+- "MET"
+- "PHE"
+- "PRO"
+- "SER"
+- "THR"
+- "TRP"
+- "TYR"
+- "VAL"
+-!entry.ALA.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.107660
+- "HA" "H1" 0 1 131072 4 1 0.039730
+- "CB" "CT" 0 1 131072 5 6 -0.131600
+- "HB1" "HC" 0 1 131072 6 1 0.074970
+- "HB2" "HC" 0 1 131072 7 1 0.074970
+- "HB3" "HC" 0 1 131072 8 1 0.074970
+- "C" "C" 0 1 131072 9 6 0.670480
+- "O" "O" 0 1 131072 10 8 -0.583250
+-!entry.ALA.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB1" "HC" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.ALA.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ALA.unit.childsequence single int
+- 2
+-!entry.ALA.unit.connect array int
+- 1
+- 9
+-!entry.ALA.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 9 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 9 10 1
+-!entry.ALA.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+-!entry.ALA.unit.name single str
+- "ALA"
+-!entry.ALA.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 3.877484 3.115795 2.131197
+- 4.075059 4.623017 1.205786
+- 2.496995 3.801075 1.241379
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.ALA.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 9 0 0 0 0
+-!entry.ALA.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "ALA" 1 11 1 "p" 0
+-!entry.ALA.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.ALA.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ALA.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.ARG.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.226630
+- "HA" "H1" 0 1 131072 4 1 0.106720
+- "CB" "CT" 0 1 131072 5 6 0.333990
+- "HB2" "HC" 0 1 131072 6 1 -0.030430
+- "HB3" "HC" 0 1 131072 7 1 -0.030430
+- "CG" "CT" 0 1 131072 8 6 -0.417310
+- "HG2" "HC" 0 1 131072 9 1 0.127030
+- "HG3" "HC" 0 1 131072 10 1 0.127030
+- "CD" "CT" 0 1 131072 11 6 0.599560
+- "HD2" "H1" 0 1 131072 12 1 -0.082670
+- "HD3" "H1" 0 1 131072 13 1 -0.082670
+- "NE" "N2" 0 1 131072 14 7 -0.785780
+- "HE" "H" 0 1 131072 15 1 0.415010
+- "CZ" "CA" 0 1 131072 16 6 1.104320
+- "NH1" "N2" 0 1 131072 17 7 -0.960300
+- "HH11" "H" 0 1 131072 18 1 0.447060
+- "HH12" "H" 0 1 131072 19 1 0.447060
+- "NH2" "N2" 0 1 131072 20 7 -0.960300
+- "HH21" "H" 0 1 131072 21 1 0.447060
+- "HH22" "H" 0 1 131072 22 1 0.447060
+- "C" "C" 0 1 131072 23 6 0.670480
+- "O" "O" 0 1 131072 24 8 -0.583250
+-!entry.ARG.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "H1" 0 -1 0.0
+- "HD3" "H1" 0 -1 0.0
+- "NE" "N2" 0 -1 0.0
+- "HE" "H" 0 -1 0.0
+- "CZ" "CA" 0 -1 0.0
+- "NH1" "N2" 0 -1 0.0
+- "HH11" "H" 0 -1 0.0
+- "HH12" "H" 0 -1 0.0
+- "NH2" "N2" 0 -1 0.0
+- "HH21" "H" 0 -1 0.0
+- "HH22" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.ARG.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ARG.unit.childsequence single int
+- 2
+-!entry.ARG.unit.connect array int
+- 1
+- 23
+-!entry.ARG.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 23 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 14 15 1
+- 14 16 1
+- 16 17 1
+- 16 20 1
+- 17 18 1
+- 17 19 1
+- 20 21 1
+- 20 22 1
+- 23 24 1
+-!entry.ARG.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+- "R" 1 "A" 24
+-!entry.ARG.unit.name single str
+- "ARG"
+-!entry.ARG.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.881105 5.817645 2.426721
+- 2.801135 5.964881 2.435959
+- 4.181626 5.279602 3.325774
+- 4.540320 7.142723 2.424483
+- 5.151805 7.375492 1.655065
+- 4.364284 8.040989 3.389382
+- 3.575026 7.807606 4.434133
+- 3.088949 6.925423 4.508848
+- 3.465367 8.513631 5.147998
+- 5.006254 9.201287 3.286991
+- 5.604855 9.375325 2.492329
+- 4.892216 9.903045 4.004368
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.ARG.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 23 0 0 0 0
+-!entry.ARG.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "ARG" 1 25 1 "p" 0
+-!entry.ARG.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.ARG.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ARG.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.ASH.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 0.002180
+- "HA" "H1" 0 1 131072 4 1 0.013640
+- "CB" "CT" 0 1 131072 5 6 -0.142020
+- "HB2" "HC" 0 1 131072 6 1 0.124360
+- "HB3" "HC" 0 1 131072 7 1 0.124360
+- "CG" "C" 0 1 131072 8 6 0.584300
+- "OD1" "O" 0 1 131072 9 8 -0.548830
+- "OD2" "OH" 0 1 131072 10 8 -0.581530
+- "HD2" "HO" 0 1 131072 11 1 0.448920
+- "C" "C" 0 1 131072 12 6 0.670480
+- "O" "O" 0 1 131072 13 8 -0.583250
+-!entry.ASH.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C" 0 -1 0.0
+- "OD1" "O" 0 -1 0.0
+- "OD2" "OH" 0 -1 0.0
+- "HD2" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.ASH.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ASH.unit.childsequence single int
+- 2
+-!entry.ASH.unit.connect array int
+- 1
+- 12
+-!entry.ASH.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 12 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 10 11 1
+- 12 13 1
+-!entry.ASH.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+-!entry.ASH.unit.name single str
+- "ASH"
+-!entry.ASH.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.275101 5.011380 1.194527
+- 3.669108 5.954940 0.620011
+- 5.407731 5.091879 1.740667
+- 5.742902 5.987179 1.652920
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.ASH.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 12 0 0 0 0
+-!entry.ASH.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "ASH" 1 14 1 "p" 0
+-!entry.ASH.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.ASH.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ASH.unit.velocities table  dbl x  dbl y  dbl z
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+- 0.0 0.0 0.0
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+-!entry.ASN.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.045790
+- "HA" "H1" 0 1 131072 4 1 0.030960
+- "CB" "CT" 0 1 131072 5 6 -0.284870
+- "HB2" "HC" 0 1 131072 6 1 0.150880
+- "HB3" "HC" 0 1 131072 7 1 0.150880
+- "CG" "C" 0 1 131072 8 6 0.619540
+- "OD1" "O" 0 1 131072 9 8 -0.546540
+- "ND2" "N" 0 1 131072 10 7 -0.812900
+- "HD21" "H" 0 1 131072 11 1 0.381610
+- "HD22" "H" 0 1 131072 12 1 0.381610
+- "C" "C" 0 1 131072 13 6 0.670480
+- "O" "O" 0 1 131072 14 8 -0.583250
+-!entry.ASN.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C" 0 -1 0.0
+- "OD1" "O" 0 -1 0.0
+- "ND2" "N" 0 -1 0.0
+- "HD21" "H" 0 -1 0.0
+- "HD22" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.ASN.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ASN.unit.childsequence single int
+- 2
+-!entry.ASN.unit.connect array int
+- 1
+- 13
+-!entry.ASN.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 13 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 10 11 1
+- 10 12 1
+- 13 14 1
+-!entry.ASN.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+-!entry.ASN.unit.name single str
+- "ASN"
+-!entry.ASN.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.253700 5.017112 1.232144
+- 5.005299 5.340406 0.315072
+- 3.984885 5.817909 2.265917
+- 4.408015 6.733702 2.314743
+- 3.359611 5.504297 2.994464
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.ASN.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 13 0 0 0 0
+-!entry.ASN.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "ASN" 1 15 1 "p" 0
+-!entry.ASN.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.ASN.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ASN.unit.velocities table  dbl x  dbl y  dbl z
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+-!entry.ASP.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.155870
+- "HA" "H1" 0 1 131072 4 1 0.001730
+- "CB" "CT" 0 1 131072 5 6 -0.175110
+- "HB2" "HC" 0 1 131072 6 1 0.072670
+- "HB3" "HC" 0 1 131072 7 1 0.072670
+- "CG" "C" 0 1 131072 8 6 0.847270
+- "OD1" "O2" 0 1 131072 9 8 -0.818990
+- "OD2" "O2" 0 1 131072 10 8 -0.818990
+- "C" "C" 0 1 131072 11 6 0.670480
+- "O" "O" 0 1 131072 12 8 -0.583250
+-!entry.ASP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C" 0 -1 0.0
+- "OD1" "O2" 0 -1 0.0
+- "OD2" "O2" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.ASP.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ASP.unit.childsequence single int
+- 2
+-!entry.ASP.unit.connect array int
+- 1
+- 11
+-!entry.ASP.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 11 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 11 12 1
+-!entry.ASP.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+-!entry.ASP.unit.name single str
+- "ASP"
+-!entry.ASP.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.275101 5.011380 1.194527
+- 3.669108 5.954940 0.620011
+- 5.407731 5.091879 1.740667
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.ASP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 11 0 0 0 0
+-!entry.ASP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "ASP" 1 13 1 "p" 0
+-!entry.ASP.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.ASP.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ASP.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+-!entry.CIM.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "CL-" "IM" 0 1 131072 1 -1 -1.000000
+-!entry.CIM.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "CL-" "IM" 0 -1 0.0
+-!entry.CIM.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CIM.unit.childsequence single int
+- 2
+-!entry.CIM.unit.connect array int
+- 1
+- 1
+-!entry.CIM.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+-!entry.CIM.unit.name single str
+- "CIM"
+-!entry.CIM.unit.positions table  dbl x  dbl y  dbl z
+- 2.000001 1.000000 -1.346410E-06
+-!entry.CIM.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 1 0 0 0 0
+-!entry.CIM.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CIM" 1 2 1 "?" 0
+-!entry.CIM.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CIM.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CIM.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+-!entry.CIP.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "NA+" "IP" 0 1 131072 1 -1 1.000000
+-!entry.CIP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "NA+" "IP" 0 -1 0.0
+-!entry.CIP.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CIP.unit.childsequence single int
+- 2
+-!entry.CIP.unit.connect array int
+- 1
+- 1
+-!entry.CIP.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+-!entry.CIP.unit.name single str
+- "CIP"
+-!entry.CIP.unit.positions table  dbl x  dbl y  dbl z
+- 2.000001 1.000000 -1.346410E-06
+-!entry.CIP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 1 0 0 0 0
+-!entry.CIP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CIP" 1 2 1 "?" 0
+-!entry.CIP.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CIP.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CIP.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+-!entry.CYM.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "HN" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.218730
+- "HA" "H1" 0 1 131072 4 1 0.077600
+- "CB" "CT" 0 1 131072 5 6 0.224400
+- "HB3" "H1" 0 1 131072 6 1 -0.057150
+- "HB2" "H1" 0 1 131072 7 1 -0.057150
+- "SG" "SH" 0 1 131072 8 16 -0.943590
+- "C" "C" 0 1 131072 9 6 0.670480
+- "O" "O" 0 1 131072 10 8 -0.583250
+-!entry.CYM.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "HN" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "SG" "SH" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.CYM.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CYM.unit.childsequence single int
+- 2
+-!entry.CYM.unit.connect array int
+- 1
+- 9
+-!entry.CYM.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 9 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 9 10 1
+-!entry.CYM.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+-!entry.CYM.unit.name single str
+- "CYM"
+-!entry.CYM.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 3.877484 3.115795 2.131197
+- 2.496995 3.801075 1.241379
+- 4.309573 5.303523 1.366036
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.CYM.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 9 0 0 0 0
+-!entry.CYM.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CYM" 1 11 1 "p" 0
+-!entry.CYM.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CYM.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CYM.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CYS.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.038240
+- "HA" "H1" 0 1 131072 4 1 0.042360
+- "CB" "CT" 0 1 131072 5 6 0.012160
+- "HB2" "H1" 0 1 131072 6 1 0.051450
+- "HB3" "H1" 0 1 131072 7 1 0.051450
+- "SG" "SH" 0 1 131072 8 16 -0.245770
+- "HG" "HS" 0 1 131072 9 1 0.151970
+- "C" "C" 0 1 131072 10 6 0.670480
+- "O" "O" 0 1 131072 11 8 -0.583250
+-!entry.CYS.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "SG" "SH" 0 -1 0.0
+- "HG" "HS" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.CYS.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CYS.unit.childsequence single int
+- 2
+-!entry.CYS.unit.connect array int
+- 1
+- 10
+-!entry.CYS.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 10 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 10 11 1
+-!entry.CYS.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+-!entry.CYS.unit.name single str
+- "CYS"
+-!entry.CYS.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.309573 5.303523 1.366036
+- 3.725392 5.622018 2.517640
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.CYS.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 10 0 0 0 0
+-!entry.CYS.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CYS" 1 12 1 "p" 0
+-!entry.CYS.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CYS.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CYS.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.CYX.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.036230
+- "HA" "H1" 0 1 131072 4 1 0.016940
+- "CB" "CT" 0 1 131072 5 6 -0.039530
+- "HB2" "H1" 0 1 131072 6 1 0.081010
+- "HB3" "H1" 0 1 131072 7 1 0.081010
+- "SG" "S" 0 1 131072 8 16 -0.077820
+- "C" "C" 0 1 131072 9 6 0.670480
+- "O" "O" 0 1 131072 10 8 -0.583250
+-!entry.CYX.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "SG" "S" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.CYX.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CYX.unit.childsequence single int
+- 2
+-!entry.CYX.unit.connect array int
+- 1
+- 9
+-!entry.CYX.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 9 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 9 10 1
+-!entry.CYX.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+-!entry.CYX.unit.name single str
+- "CYX"
+-!entry.CYX.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.309573 5.303523 1.366036
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.CYX.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 9 8 0 0 0
+-!entry.CYX.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "CYX" 1 11 1 "p" 0
+-!entry.CYX.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.CYX.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.CYX.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+-!entry.GLH.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.137720
+- "HA" "H1" 0 1 131072 4 1 0.067770
+- "CB" "CT" 0 1 131072 5 6 0.139840
+- "HB2" "HC" 0 1 131072 6 1 0.014650
+- "HB3" "HC" 0 1 131072 7 1 0.014650
+- "CG" "CT" 0 1 131072 8 6 -0.360940
+- "HG2" "HC" 0 1 131072 9 1 0.184800
+- "HG3" "HC" 0 1 131072 10 1 0.184800
+- "CD" "C" 0 1 131072 11 6 0.639100
+- "OE1" "O" 0 1 131072 12 8 -0.571870
+- "OE2" "OH" 0 1 131072 13 8 -0.605840
+- "HE2" "HO" 0 1 131072 14 1 0.456140
+- "C" "C" 0 1 131072 15 6 0.670480
+- "O" "O" 0 1 131072 16 8 -0.583250
+-!entry.GLH.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "C" 0 -1 0.0
+- "OE1" "O" 0 -1 0.0
+- "OE2" "OH" 0 -1 0.0
+- "HE2" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.GLH.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.GLH.unit.childsequence single int
+- 2
+-!entry.GLH.unit.connect array int
+- 1
+- 15
+-!entry.GLH.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 15 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 15 16 1
+-!entry.GLH.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+-!entry.GLH.unit.name single str
+- "GLH"
+-!entry.GLH.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.267328 4.996267 1.194946
+- 5.347413 4.849843 1.186158
+- 3.966923 5.535124 0.296342
+- 3.873732 5.805369 2.428706
+- 4.594590 5.679012 3.454376
+- 2.855965 6.542070 2.333721
+- 2.710526 6.996624 3.166684
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.GLH.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 15 0 0 0 0
+-!entry.GLH.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "GLH" 1 17 1 "p" 0
+-!entry.GLH.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.GLH.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.GLH.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.GLN.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.239260
+- "HA" "H1" 0 1 131072 4 1 0.070250
+- "CB" "CT" 0 1 131072 5 6 0.515970
+- "HB2" "HC" 0 1 131072 6 1 -0.085650
+- "HB3" "HC" 0 1 131072 7 1 -0.085650
+- "CG" "CT" 0 1 131072 8 6 -0.728430
+- "HG2" "HC" 0 1 131072 9 1 0.258090
+- "HG3" "HC" 0 1 131072 10 1 0.258090
+- "CD" "C" 0 1 131072 11 6 0.823540
+- "OE1" "O" 0 1 131072 12 8 -0.668550
+- "NE2" "N" 0 1 131072 13 7 -0.858360
+- "HE21" "H" 0 1 131072 14 1 0.382670
+- "HE22" "H" 0 1 131072 15 1 0.382670
+- "C" "C" 0 1 131072 16 6 0.670480
+- "O" "O" 0 1 131072 17 8 -0.583250
+-!entry.GLN.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "C" 0 -1 0.0
+- "OE1" "O" 0 -1 0.0
+- "NE2" "N" 0 -1 0.0
+- "HE21" "H" 0 -1 0.0
+- "HE22" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.GLN.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.GLN.unit.childsequence single int
+- 2
+-!entry.GLN.unit.connect array int
+- 1
+- 16
+-!entry.GLN.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 16 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+- 16 17 1
+-!entry.GLN.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+-!entry.GLN.unit.name single str
+- "GLN"
+-!entry.GLN.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.906976 5.848443 2.410302
+- 3.138962 5.408349 3.262893
+- 4.458856 7.061523 2.488333
+- 4.248434 7.659045 3.274966
+- 5.084281 7.376210 1.760379
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.GLN.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 16 0 0 0 0
+-!entry.GLN.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "GLN" 1 18 1 "p" 0
+-!entry.GLN.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.GLN.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.GLN.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.GLU.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.348150
+- "HA" "H1" 0 1 131072 4 1 0.126380
+- "CB" "CT" 0 1 131072 5 6 0.696480
+- "HB2" "HC" 0 1 131072 6 1 -0.186180
+- "HB3" "HC" 0 1 131072 7 1 -0.186180
+- "CG" "CT" 0 1 131072 8 6 -0.662250
+- "HG2" "HC" 0 1 131072 9 1 0.193310
+- "HG3" "HC" 0 1 131072 10 1 0.193310
+- "CD" "C" 0 1 131072 11 6 0.804540
+- "OE1" "O2" 0 1 131072 12 8 -0.802940
+- "OE2" "O2" 0 1 131072 13 8 -0.802940
+- "C" "C" 0 1 131072 14 6 0.670480
+- "O" "O" 0 1 131072 15 8 -0.583250
+-!entry.GLU.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "C" 0 -1 0.0
+- "OE1" "O2" 0 -1 0.0
+- "OE2" "O2" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.GLU.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.GLU.unit.childsequence single int
+- 2
+-!entry.GLU.unit.connect array int
+- 1
+- 14
+-!entry.GLU.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 14 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 14 15 1
+-!entry.GLU.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+-!entry.GLU.unit.name single str
+- "GLU"
+-!entry.GLU.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.267328 4.996267 1.194946
+- 5.347413 4.849843 1.186158
+- 3.966923 5.535124 0.296342
+- 3.873732 5.805369 2.428706
+- 4.594590 5.679012 3.454376
+- 2.855965 6.542070 2.333721
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.GLU.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 14 0 0 0 0
+-!entry.GLU.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "GLU" 1 16 1 "p" 0
+-!entry.GLU.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.GLU.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.GLU.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.GLY.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.277560
+- "HA2" "H0" 0 1 131072 4 -1 0.151470
+- "HA3" "H0" 0 1 131072 5 -1 0.151470
+- "C" "C" 0 1 131072 6 6 0.670480
+- "O" "O" 0 1 131072 7 8 -0.583250
+-!entry.GLY.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA2" "H0" 0 -1 0.0
+- "HA3" "H0" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.GLY.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.GLY.unit.childsequence single int
+- 2
+-!entry.GLY.unit.connect array int
+- 1
+- 6
+-!entry.GLY.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 6 1
+- 6 7 1
+-!entry.GLY.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+-!entry.GLY.unit.name single str
+- "GLY"
+-!entry.GLY.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.671668 3.400125 0.889824
+- 5.483710 2.686702 -4.438857E-06
+- 5.993369 1.568360 -8.469843E-06
+-!entry.GLY.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 6 0 0 0 0
+-!entry.GLY.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "GLY" 1 8 1 "p" 0
+-!entry.GLY.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.GLY.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.GLY.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.HID.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.046110
+- "HA" "H1" 0 1 131072 4 1 -0.008910
+- "CB" "CT" 0 1 131072 5 6 -0.213070
+- "HB2" "HC" 0 1 131072 6 1 0.111650
+- "HB3" "HC" 0 1 131072 7 1 0.111650
+- "CG" "CC" 0 1 131072 8 6 0.275120
+- "ND1" "NA" 0 1 131072 9 7 -0.364930
+- "HD1" "H" 0 1 131072 10 1 0.352330
+- "CE1" "CR" 0 1 131072 11 6 0.226080
+- "HE1" "H5" 0 1 131072 12 1 0.060700
+- "NE2" "NB" 0 1 131072 13 7 -0.504470
+- "CD2" "CV" 0 1 131072 14 6 -0.070100
+- "HD2" "H4" 0 1 131072 15 1 0.095440
+- "C" "C" 0 1 131072 16 6 0.670480
+- "O" "O" 0 1 131072 17 8 -0.583250
+-!entry.HID.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CC" 0 -1 0.0
+- "ND1" "NA" 0 -1 0.0
+- "HD1" "H" 0 -1 0.0
+- "CE1" "CR" 0 -1 0.0
+- "HE1" "H5" 0 -1 0.0
+- "NE2" "NB" 0 -1 0.0
+- "CD2" "CV" 0 -1 0.0
+- "HD2" "H4" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.HID.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.HID.unit.childsequence single int
+- 2
+-!entry.HID.unit.connect array int
+- 1
+- 16
+-!entry.HID.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 16 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 14 1
+- 9 10 1
+- 9 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 14 15 1
+- 16 17 1
+-!entry.HID.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+-!entry.HID.unit.name single str
+- "HID"
+-!entry.HID.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.942782 5.885086 2.382972
+- 3.339725 5.691913 3.169805
+- 4.624274 6.997642 2.182500
+- 4.563048 7.811875 2.904563
+- 5.294011 6.891451 1.061663
+- 5.058974 5.678868 0.492453
+- 5.537741 5.417846 -0.451343
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.HID.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 16 0 0 0 0
+-!entry.HID.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "HID" 1 18 1 "p" 0
+-!entry.HID.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.HID.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.HID.unit.velocities table  dbl x  dbl y  dbl z
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+-!entry.HIE.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.125440
+- "HA" "H1" 0 1 131072 4 1 0.030840
+- "CB" "CT" 0 1 131072 5 6 -0.214440
+- "HB2" "HC" 0 1 131072 6 1 0.140600
+- "HB3" "HC" 0 1 131072 7 1 0.140600
+- "CG" "CC" 0 1 131072 8 6 0.385250
+- "ND1" "NB" 0 1 131072 9 7 -0.681670
+- "CE1" "CR" 0 1 131072 10 6 0.349170
+- "HE1" "H5" 0 1 131072 11 1 0.030760
+- "NE2" "NA" 0 1 131072 12 7 -0.327570
+- "HE2" "H" 0 1 131072 13 1 0.341080
+- "CD2" "CW" 0 1 131072 14 6 -0.206690
+- "HD2" "H4" 0 1 131072 15 1 0.162890
+- "C" "C" 0 1 131072 16 6 0.670480
+- "O" "O" 0 1 131072 17 8 -0.583250
+-!entry.HIE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CC" 0 -1 0.0
+- "ND1" "NB" 0 -1 0.0
+- "CE1" "CR" 0 -1 0.0
+- "HE1" "H5" 0 -1 0.0
+- "NE2" "NA" 0 -1 0.0
+- "HE2" "H" 0 -1 0.0
+- "CD2" "CW" 0 -1 0.0
+- "HD2" "H4" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.HIE.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.HIE.unit.childsequence single int
+- 2
+-!entry.HIE.unit.connect array int
+- 1
+- 16
+-!entry.HIE.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 16 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 14 1
+- 9 10 1
+- 10 11 1
+- 10 12 1
+- 12 13 1
+- 12 14 1
+- 14 15 1
+- 16 17 1
+-!entry.HIE.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+-!entry.HIE.unit.name single str
+- "HIE"
+-!entry.HIE.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.942782 5.885086 2.382972
+- 4.624274 6.997642 2.182500
+- 4.563048 7.811875 2.904563
+- 5.294011 6.891451 1.061663
+- 5.896297 7.605085 0.676854
+- 5.058974 5.678868 0.492453
+- 5.537741 5.417846 -0.451343
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.HIE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 16 0 0 0 0
+-!entry.HIE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "HIE" 1 18 1 "p" 0
+-!entry.HIE.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.HIE.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.HIE.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+-!entry.HIP.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 0.017840
+- "HA" "H1" 0 1 131072 4 1 -0.000340
+- "CB" "CT" 0 1 131072 5 6 -0.074410
+- "HB2" "HC" 0 1 131072 6 1 0.084140
+- "HB3" "HC" 0 1 131072 7 1 0.084140
+- "CG" "CC" 0 1 131072 8 6 0.259530
+- "ND1" "NA" 0 1 131072 9 7 -0.134860
+- "HD1" "H" 0 1 131072 10 1 0.376730
+- "CE1" "CR" 0 1 131072 11 6 -0.086920
+- "HE1" "H5" 0 1 131072 12 1 0.197160
+- "NE2" "NA" 0 1 131072 13 7 0.089780
+- "HE2" "H" 0 1 131072 14 1 0.285300
+- "CD2" "CW" 0 1 131072 15 6 -0.259230
+- "HD2" "H4" 0 1 131072 16 1 0.186520
+- "C" "C" 0 1 131072 17 6 0.670480
+- "O" "O" 0 1 131072 18 8 -0.583250
+-!entry.HIP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CC" 0 -1 0.0
+- "ND1" "NA" 0 -1 0.0
+- "HD1" "H" 0 -1 0.0
+- "CE1" "CR" 0 -1 0.0
+- "HE1" "H5" 0 -1 0.0
+- "NE2" "NA" 0 -1 0.0
+- "HE2" "H" 0 -1 0.0
+- "CD2" "CW" 0 -1 0.0
+- "HD2" "H4" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.HIP.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.HIP.unit.childsequence single int
+- 2
+-!entry.HIP.unit.connect array int
+- 1
+- 17
+-!entry.HIP.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 17 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 15 1
+- 9 10 1
+- 9 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+- 17 18 1
+-!entry.HIP.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+-!entry.HIP.unit.name single str
+- "HIP"
+-!entry.HIP.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.942782 5.885086 2.382972
+- 3.339725 5.691913 3.169805
+- 4.624274 6.997642 2.182500
+- 4.563048 7.811875 2.904563
+- 5.294011 6.891451 1.061663
+- 5.896297 7.605085 0.676854
+- 5.058974 5.678868 0.492453
+- 5.537741 5.417846 -0.451343
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.HIP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 17 0 0 0 0
+-!entry.HIP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "HIP" 1 19 1 "p" 0
+-!entry.HIP.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.HIP.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.HIP.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.ILE.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.319670
+- "HA" "H1" 0 1 131072 4 1 0.149580
+- "CB" "CT" 0 1 131072 5 6 0.330640
+- "HB" "HC" 0 1 131072 6 1 -0.064360
+- "CG2" "CT" 0 1 131072 7 6 -0.412720
+- "HG21" "HC" 0 1 131072 8 1 0.117730
+- "HG22" "HC" 0 1 131072 9 1 0.117730
+- "HG23" "HC" 0 1 131072 10 1 0.117730
+- "CG1" "CT" 0 1 131072 11 6 -0.127860
+- "HG12" "HC" 0 1 131072 12 1 0.051810
+- "HG13" "HC" 0 1 131072 13 1 0.051810
+- "CD1" "CT" 0 1 131072 14 6 -0.024360
+- "HD11" "HC" 0 1 131072 15 1 0.012440
+- "HD12" "HC" 0 1 131072 16 1 0.012440
+- "HD13" "HC" 0 1 131072 17 1 0.012440
+- "C" "C" 0 1 131072 18 6 0.670480
+- "O" "O" 0 1 131072 19 8 -0.583250
+-!entry.ILE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB" "HC" 0 -1 0.0
+- "CG2" "CT" 0 -1 0.0
+- "HG21" "HC" 0 -1 0.0
+- "HG22" "HC" 0 -1 0.0
+- "HG23" "HC" 0 -1 0.0
+- "CG1" "CT" 0 -1 0.0
+- "HG12" "HC" 0 -1 0.0
+- "HG13" "HC" 0 -1 0.0
+- "CD1" "CT" 0 -1 0.0
+- "HD11" "HC" 0 -1 0.0
+- "HD12" "HC" 0 -1 0.0
+- "HD13" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.ILE.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ILE.unit.childsequence single int
+- 2
+-!entry.ILE.unit.connect array int
+- 1
+- 18
+-!entry.ILE.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 18 1
+- 5 6 1
+- 5 7 1
+- 5 11 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 14 15 1
+- 14 16 1
+- 14 17 1
+- 18 19 1
+-!entry.ILE.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+-!entry.ILE.unit.name single str
+- "ILE"
+-!entry.ILE.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.552136 3.620733 1.245168
+- 2.470128 3.752486 1.245640
+- 3.970045 2.845728 2.490296
+- 5.052053 2.713974 2.490763
+- 3.671561 3.399208 3.380615
+- 3.485650 1.869275 2.490737
+- 4.230204 4.986694 1.245169
+- 5.312310 4.855746 1.245164
+- 3.931820 5.541027 0.355348
+- 3.812294 5.761632 2.490339
+- 4.110777 5.208104 3.380628
+- 4.296689 6.738085 2.490833
+- 2.730286 5.893383 2.490813
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.ILE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 18 0 0 0 0
+-!entry.ILE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "ILE" 1 20 1 "p" 0
+-!entry.ILE.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.ILE.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.ILE.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.LEU.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.116580
+- "HA" "H1" 0 1 131072 4 1 0.026810
+- "CB" "CT" 0 1 131072 5 6 -0.227760
+- "HB2" "HC" 0 1 131072 6 1 0.095470
+- "HB3" "HC" 0 1 131072 7 1 0.095470
+- "CG" "CT" 0 1 131072 8 6 0.606550
+- "HG" "HC" 0 1 131072 9 1 -0.114060
+- "CD1" "CT" 0 1 131072 10 6 -0.794260
+- "HD11" "HC" 0 1 131072 11 1 0.208000
+- "HD12" "HC" 0 1 131072 12 1 0.208000
+- "HD13" "HC" 0 1 131072 13 1 0.208000
+- "CD2" "CT" 0 1 131072 14 6 -0.794260
+- "HD21" "HC" 0 1 131072 15 1 0.208000
+- "HD22" "HC" 0 1 131072 16 1 0.208000
+- "HD23" "HC" 0 1 131072 17 1 0.208000
+- "C" "C" 0 1 131072 18 6 0.670480
+- "O" "O" 0 1 131072 19 8 -0.583250
+-!entry.LEU.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG" "HC" 0 -1 0.0
+- "CD1" "CT" 0 -1 0.0
+- "HD11" "HC" 0 -1 0.0
+- "HD12" "HC" 0 -1 0.0
+- "HD13" "HC" 0 -1 0.0
+- "CD2" "CT" 0 -1 0.0
+- "HD21" "HC" 0 -1 0.0
+- "HD22" "HC" 0 -1 0.0
+- "HD23" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.LEU.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.LEU.unit.childsequence single int
+- 2
+-!entry.LEU.unit.connect array int
+- 1
+- 18
+-!entry.LEU.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 18 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 14 1
+- 10 11 1
+- 10 12 1
+- 10 13 1
+- 14 15 1
+- 14 16 1
+- 14 17 1
+- 18 19 1
+-!entry.LEU.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+-!entry.LEU.unit.name single str
+- "LEU"
+-!entry.LEU.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.853429 5.762895 -0.062857
+- 2.773449 5.910113 -0.054557
+- 4.351513 6.732052 -0.090203
+- 4.134159 5.185704 -0.943846
+- 3.881105 5.817645 2.426721
+- 4.181626 5.279602 3.325774
+- 4.379198 6.786825 2.400363
+- 2.801135 5.964881 2.435959
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.LEU.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 18 0 0 0 0
+-!entry.LEU.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "LEU" 1 20 1 "p" 0
+-!entry.LEU.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.LEU.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.LEU.unit.velocities table  dbl x  dbl y  dbl z
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+-!entry.LYN.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.181890
+- "HA" "H1" 0 1 131072 4 1 0.074160
+- "CB" "CT" 0 1 131072 5 6 0.078320
+- "HB2" "HC" 0 1 131072 6 1 -0.000500
+- "HB3" "HC" 0 1 131072 7 1 -0.000500
+- "CG" "CT" 0 1 131072 8 6 0.004490
+- "HG2" "HC" 0 1 131072 9 1 0.023890
+- "HG3" "HC" 0 1 131072 10 1 0.023890
+- "CD" "CT" 0 1 131072 11 6 -0.277170
+- "HD2" "HC" 0 1 131072 12 1 0.112690
+- "HD3" "HC" 0 1 131072 13 1 0.112690
+- "CE" "CT" 0 1 131072 14 6 0.554010
+- "HE2" "H1" 0 1 131072 15 1 -0.114200
+- "HE3" "H1" 0 1 131072 16 1 -0.114200
+- "NZ" "NT" 0 1 131072 17 7 -0.979220
+- "HZ2" "H" 0 1 131072 18 1 0.354460
+- "HZ3" "H" 0 1 131072 19 1 0.354460
+- "C" "C" 0 1 131072 20 6 0.670480
+- "O" "O" 0 1 131072 21 8 -0.583250
+-!entry.LYN.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "HC" 0 -1 0.0
+- "HD3" "HC" 0 -1 0.0
+- "CE" "CT" 0 -1 0.0
+- "HE2" "H1" 0 -1 0.0
+- "HE3" "H1" 0 -1 0.0
+- "NZ" "NT" 0 -1 0.0
+- "HZ2" "H" 0 -1 0.0
+- "HZ3" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.LYN.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.LYN.unit.childsequence single int
+- 2
+-!entry.LYN.unit.connect array int
+- 1
+- 20
+-!entry.LYN.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 20 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 14 15 1
+- 14 16 1
+- 14 17 1
+- 17 18 1
+- 17 19 1
+- 20 21 1
+-!entry.LYN.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+-!entry.LYN.unit.name single str
+- "LYN"
+-!entry.LYN.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.881105 5.817645 2.426721
+- 2.801135 5.964881 2.435959
+- 4.181626 5.279602 3.325774
+- 4.578325 7.173410 2.389153
+- 5.658410 7.026987 2.380363
+- 4.277917 7.712267 1.490550
+- 4.199422 7.952309 3.576860
+- 4.661186 8.850226 3.551979
+- 3.198675 8.088466 3.584971
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.LYN.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 20 0 0 0 0
+-!entry.LYN.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "LYN" 1 22 1 "p" 0
+-!entry.LYN.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.LYN.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.LYN.unit.velocities table  dbl x  dbl y  dbl z
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+- 0.0 0.0 0.0
+-!entry.LYS.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.181230
+- "HA" "H1" 0 1 131072 4 1 0.099160
+- "CB" "CT" 0 1 131072 5 6 0.004110
+- "HB2" "HC" 0 1 131072 6 1 0.027580
+- "HB3" "HC" 0 1 131072 7 1 0.027580
+- "CG" "CT" 0 1 131072 8 6 -0.053270
+- "HG2" "HC" 0 1 131072 9 1 0.053050
+- "HG3" "HC" 0 1 131072 10 1 0.053050
+- "CD" "CT" 0 1 131072 11 6 -0.201370
+- "HD2" "HC" 0 1 131072 12 1 0.095630
+- "HD3" "HC" 0 1 131072 13 1 0.095630
+- "CE" "CT" 0 1 131072 14 6 0.465480
+- "HE2" "HP" 0 1 131072 15 1 -0.049170
+- "HE3" "HP" 0 1 131072 16 1 -0.049170
+- "NZ" "N3" 0 1 131072 17 7 -0.366380
+- "HZ1" "H" 0 1 131072 18 1 0.334900
+- "HZ2" "H" 0 1 131072 19 1 0.334900
+- "HZ3" "H" 0 1 131072 20 1 0.334900
+- "C" "C" 0 1 131072 21 6 0.670480
+- "O" "O" 0 1 131072 22 8 -0.583250
+-!entry.LYS.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "HC" 0 -1 0.0
+- "HD3" "HC" 0 -1 0.0
+- "CE" "CT" 0 -1 0.0
+- "HE2" "HP" 0 -1 0.0
+- "HE3" "HP" 0 -1 0.0
+- "NZ" "N3" 0 -1 0.0
+- "HZ1" "H" 0 -1 0.0
+- "HZ2" "H" 0 -1 0.0
+- "HZ3" "H" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.LYS.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.LYS.unit.childsequence single int
+- 2
+-!entry.LYS.unit.connect array int
+- 1
+- 21
+-!entry.LYS.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 21 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 14 15 1
+- 14 16 1
+- 14 17 1
+- 17 18 1
+- 17 19 1
+- 17 20 1
+- 21 22 1
+-!entry.LYS.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+-!entry.LYS.unit.name single str
+- "LYS"
+-!entry.LYS.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.881105 5.817645 2.426721
+- 2.801135 5.964881 2.435959
+- 4.181626 5.279602 3.325774
+- 4.578325 7.173410 2.389153
+- 5.658410 7.026987 2.380363
+- 4.277917 7.712267 1.490550
+- 4.199422 7.952309 3.576860
+- 4.478085 7.453366 4.409628
+- 4.661186 8.850226 3.551979
+- 3.198675 8.088466 3.584971
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.LYS.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 21 0 0 0 0
+-!entry.LYS.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "LYS" 1 23 1 "p" 0
+-!entry.LYS.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.LYS.unit.solventcap array dbl
+- -1.000000
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+- 0.0
+- 0.0
+- 0.0
+-!entry.LYS.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.MET.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.152290
+- "HA" "H1" 0 1 131072 4 1 0.080630
+- "CB" "CT" 0 1 131072 5 6 0.271900
+- "HB2" "HC" 0 1 131072 6 1 -0.049340
+- "HB3" "HC" 0 1 131072 7 1 -0.049340
+- "CG" "CT" 0 1 131072 8 6 -0.289240
+- "HG2" "H1" 0 1 131072 9 1 0.138580
+- "HG3" "H1" 0 1 131072 10 1 0.138580
+- "SD" "S" 0 1 131072 11 16 -0.127450
+- "CE" "CT" 0 1 131072 12 6 -0.275560
+- "HE1" "H1" 0 1 131072 13 1 0.112970
+- "HE2" "H1" 0 1 131072 14 1 0.112970
+- "HE3" "H1" 0 1 131072 15 1 0.112970
+- "C" "C" 0 1 131072 16 6 0.670480
+- "O" "O" 0 1 131072 17 8 -0.583250
+-!entry.MET.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "H1" 0 -1 0.0
+- "HG3" "H1" 0 -1 0.0
+- "SD" "S" 0 -1 0.0
+- "CE" "CT" 0 -1 0.0
+- "HE1" "H1" 0 -1 0.0
+- "HE2" "H1" 0 -1 0.0
+- "HE3" "H1" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.MET.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.MET.unit.childsequence single int
+- 2
+-!entry.MET.unit.connect array int
+- 1
+- 16
+-!entry.MET.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 16 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 12 13 1
+- 12 14 1
+- 12 15 1
+- 16 17 1
+-!entry.MET.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+-!entry.MET.unit.name single str
+- "MET"
+-!entry.MET.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.274186 5.009602 1.194577
+- 5.354271 4.863178 1.185788
+- 3.973781 5.548460 0.295972
+- 3.817309 5.981266 2.651708
+- 4.753212 7.463128 2.340949
+- 4.433582 7.904044 1.396741
+- 4.585907 8.175299 3.148985
+- 5.814074 7.218763 2.286554
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.MET.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 16 0 0 0 0
+-!entry.MET.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "MET" 1 18 1 "p" 0
+-!entry.MET.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.MET.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.MET.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.PHE.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.097530
+- "HA" "H1" 0 1 131072 4 1 0.021040
+- "CB" "CT" 0 1 131072 5 6 -0.127300
+- "HB2" "HC" 0 1 131072 6 1 0.103640
+- "HB3" "HC" 0 1 131072 7 1 0.103640
+- "CG" "CA" 0 1 131072 8 6 0.128890
+- "CD1" "CA" 0 1 131072 9 6 -0.194310
+- "HD1" "HA" 0 1 131072 10 1 0.141910
+- "CE1" "CA" 0 1 131072 11 6 -0.098170
+- "HE1" "HA" 0 1 131072 12 1 0.108820
+- "CZ" "CA" 0 1 131072 13 6 -0.112640
+- "HZ" "HA" 0 1 131072 14 1 0.089140
+- "CE2" "CA" 0 1 131072 15 6 -0.098170
+- "HE2" "HA" 0 1 131072 16 1 0.108820
+- "CD2" "CA" 0 1 131072 17 6 -0.194310
+- "HD2" "HA" 0 1 131072 18 1 0.141910
+- "C" "C" 0 1 131072 19 6 0.670480
+- "O" "O" 0 1 131072 20 8 -0.583250
+-!entry.PHE.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CA" 0 -1 0.0
+- "CD1" "CA" 0 -1 0.0
+- "HD1" "HA" 0 -1 0.0
+- "CE1" "CA" 0 -1 0.0
+- "HE1" "HA" 0 -1 0.0
+- "CZ" "CA" 0 -1 0.0
+- "HZ" "HA" 0 -1 0.0
+- "CE2" "CA" 0 -1 0.0
+- "HE2" "HA" 0 -1 0.0
+- "CD2" "CA" 0 -1 0.0
+- "HD2" "HA" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.PHE.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.PHE.unit.childsequence single int
+- 2
+-!entry.PHE.unit.connect array int
+- 1
+- 19
+-!entry.PHE.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 19 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 17 1
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+- 9 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 15 1
+- 15 16 1
+- 15 17 1
+- 17 18 1
+- 19 20 1
+-!entry.PHE.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+-!entry.PHE.unit.name single str
+- "PHE"
+-!entry.PHE.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 3.911613 5.857250 2.409890
+- 3.236123 5.513843 3.193398
+- 4.490014 7.129513 2.492354
+- 4.264853 7.776651 3.340066
+- 5.357616 7.570591 1.486016
+- 5.807943 8.561138 1.550220
+- 5.646818 6.739407 0.397211
+- 6.322309 7.082817 -0.386295
+- 5.068419 5.467143 0.314744
+- 5.293584 4.820007 -0.532968
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.PHE.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 19 0 0 0 0
+-!entry.PHE.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "PHE" 1 21 1 "p" 0
+-!entry.PHE.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.PHE.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.PHE.unit.velocities table  dbl x  dbl y  dbl z
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+-!entry.PRO.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.259820
+- "CD" "CT" 0 1 131072 2 6 0.070890
+- "HD2" "H1" 0 1 131072 3 1 0.019250
+- "HD3" "H1" 0 1 131072 4 1 0.019260
+- "CG" "CT" 0 1 131072 5 6 0.067960
+- "HG2" "HC" 0 1 131072 6 1 0.009600
+- "HG3" "HC" 0 1 131072 7 1 0.009600
+- "CB" "CT" 0 1 131072 8 6 0.038490
+- "HB2" "HC" 0 1 131072 9 1 0.020120
+- "HB3" "HC" 0 1 131072 10 1 0.020120
+- "CA" "CT" 0 1 131072 11 6 -0.194650
+- "HA" "H1" 0 1 131072 12 1 0.091950
+- "C" "C" 0 1 131072 13 6 0.670480
+- "O" "O" 0 1 131072 14 8 -0.583250
+-!entry.PRO.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "CD" "CT" 0 -1 0.0
+- "HD2" "H1" 0 -1 0.0
+- "HD3" "H1" 0 -1 0.0
+- "CG" "CT" 0 -1 0.0
+- "HG2" "HC" 0 -1 0.0
+- "HG3" "HC" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.PRO.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.PRO.unit.childsequence single int
+- 2
+-!entry.PRO.unit.connect array int
+- 1
+- 13
+-!entry.PRO.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 11 1
+- 2 3 1
+- 2 4 1
+- 2 5 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 10 1
+- 8 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+-!entry.PRO.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+-!entry.PRO.unit.name single str
+- "PRO"
+-!entry.PRO.unit.positions table  dbl x  dbl y  dbl z
+- 3.326834 1.557389 -1.603945E-06
+- 4.302147 0.476598 0.080119
+- 4.419998 0.019283 -0.902263
+- 3.955888 -0.274040 0.790574
+- 5.547126 1.172441 0.544693
+- 6.413549 0.741636 0.042879
+- 5.652950 1.047934 1.622376
+- 5.369091 2.628184 0.185227
+- 5.969289 2.861861 -0.694123
+- 5.690642 3.251038 1.019947
+- 3.933610 2.871277 -0.104508
+- 3.611470 3.488570 0.734106
+- 3.505164 3.526392 -1.409783
+- 2.754240 2.939065 -2.185412
+-!entry.PRO.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 13 0 0 0 0
+-!entry.PRO.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "PRO" 1 15 1 "p" 0
+-!entry.PRO.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.PRO.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.PRO.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+-!entry.SER.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.066190
+- "HA" "H1" 0 1 131072 4 1 0.078820
+- "CB" "CT" 0 1 131072 5 6 0.185370
+- "HB2" "H1" 0 1 131072 6 1 0.025410
+- "HB3" "H1" 0 1 131072 7 1 0.025410
+- "OG" "OH" 0 1 131072 8 8 -0.602470
+- "HG" "HO" 0 1 131072 9 1 0.379030
+- "C" "C" 0 1 131072 10 6 0.670480
+- "O" "O" 0 1 131072 11 8 -0.583250
+-!entry.SER.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "H1" 0 -1 0.0
+- "HB3" "H1" 0 -1 0.0
+- "OG" "OH" 0 -1 0.0
+- "HG" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.SER.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.SER.unit.childsequence single int
+- 2
+-!entry.SER.unit.connect array int
+- 1
+- 10
+-!entry.SER.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 10 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 10 11 1
+-!entry.SER.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+-!entry.SER.unit.name single str
+- "SER"
+-!entry.SER.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.230753 4.925145 1.196917
+- 3.983305 5.433814 1.972562
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.SER.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 10 0 0 0 0
+-!entry.SER.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "SER" 1 12 1 "p" 0
+-!entry.SER.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.SER.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.SER.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.THR.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.022270
+- "HA" "H1" 0 1 131072 4 1 0.053100
+- "CB" "CT" 0 1 131072 5 6 0.522850
+- "HB" "H1" 0 1 131072 6 1 -0.139050
+- "CG2" "CT" 0 1 131072 7 6 -0.588650
+- "HG21" "HC" 0 1 131072 8 1 0.162040
+- "HG22" "HC" 0 1 131072 9 1 0.162040
+- "HG23" "HC" 0 1 131072 10 1 0.162040
+- "OG1" "OH" 0 1 131072 11 8 -0.739400
+- "HG1" "HO" 0 1 131072 12 1 0.452680
+- "C" "C" 0 1 131072 13 6 0.670480
+- "O" "O" 0 1 131072 14 8 -0.583250
+-!entry.THR.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB" "H1" 0 -1 0.0
+- "CG2" "CT" 0 -1 0.0
+- "HG21" "HC" 0 -1 0.0
+- "HG22" "HC" 0 -1 0.0
+- "HG23" "HC" 0 -1 0.0
+- "OG1" "OH" 0 -1 0.0
+- "HG1" "HO" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.THR.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.THR.unit.childsequence single int
+- 2
+-!entry.THR.unit.connect array int
+- 1
+- 13
+-!entry.THR.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 13 1
+- 5 6 1
+- 5 7 1
+- 5 11 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 11 12 1
+- 13 14 1
+-!entry.THR.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+-!entry.THR.unit.name single str
+- "THR"
+-!entry.THR.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 4.075059 4.623017 1.205786
+- 2.065936 3.859425 1.244383
+- 1.567127 2.890627 1.271209
+- 1.784431 4.436953 2.124903
+- 1.764699 4.397847 0.345796
+- 3.971501 2.947413 2.411212
+- 3.724052 3.456082 3.186857
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.THR.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 13 0 0 0 0
+-!entry.THR.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "THR" 1 15 1 "p" 0
+-!entry.THR.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.THR.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.THR.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
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+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.TRP.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.094050
+- "HA" "H1" 0 1 131072 4 1 0.058350
+- "CB" "CT" 0 1 131072 5 6 0.034010
+- "HB2" "HC" 0 1 131072 6 1 0.031520
+- "HB3" "HC" 0 1 131072 7 1 0.031520
+- "CG" "C*" 0 1 131072 8 6 -0.279060
+- "CD1" "CW" 0 1 131072 9 6 0.030520
+- "HD1" "H4" 0 1 131072 10 1 0.136990
+- "NE1" "NA" 0 1 131072 11 7 -0.483180
+- "HE1" "H" 0 1 131072 12 1 0.393090
+- "CE2" "CN" 0 1 131072 13 6 0.203200
+- "CZ2" "CA" 0 1 131072 14 6 -0.272110
+- "HZ2" "HA" 0 1 131072 15 1 0.185390
+- "CH2" "CA" 0 1 131072 16 6 -0.171160
+- "HH2" "HA" 0 1 131072 17 1 0.105360
+- "CZ3" "CA" 0 1 131072 18 6 -0.058970
+- "HZ3" "HA" 0 1 131072 19 1 0.088920
+- "CE3" "CA" 0 1 131072 20 6 -0.403270
+- "HE3" "HA" 0 1 131072 21 1 0.216660
+- "CD2" "CB" 0 1 131072 22 6 0.271650
+- "C" "C" 0 1 131072 23 6 0.670480
+- "O" "O" 0 1 131072 24 8 -0.583250
+-!entry.TRP.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "C*" 0 -1 0.0
+- "CD1" "CW" 0 -1 0.0
+- "HD1" "H4" 0 -1 0.0
+- "NE1" "NA" 0 -1 0.0
+- "HE1" "H" 0 -1 0.0
+- "CE2" "CN" 0 -1 0.0
+- "CZ2" "CA" 0 -1 0.0
+- "HZ2" "HA" 0 -1 0.0
+- "CH2" "CA" 0 -1 0.0
+- "HH2" "HA" 0 -1 0.0
+- "CZ3" "CA" 0 -1 0.0
+- "HZ3" "HA" 0 -1 0.0
+- "CE3" "CA" 0 -1 0.0
+- "HE3" "HA" 0 -1 0.0
+- "CD2" "CB" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.TRP.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.TRP.unit.childsequence single int
+- 2
+-!entry.TRP.unit.connect array int
+- 1
+- 23
+-!entry.TRP.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 23 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 22 1
+- 9 10 1
+- 9 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 22 1
+- 14 15 1
+- 14 16 1
+- 16 17 1
+- 16 18 1
+- 18 19 1
+- 18 20 1
+- 20 21 1
+- 20 22 1
+- 23 24 1
+-!entry.TRP.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+- "R" 1 "A" 22
+- "R" 1 "A" 23
+- "R" 1 "A" 24
+-!entry.TRP.unit.name single str
+- "TRP"
+-!entry.TRP.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.200813 5.026064 1.321087
+- 4.023453 5.931084 2.293240
+- 3.368841 5.705466 3.135071
+- 4.811943 7.073555 1.949808
+- 4.882921 7.922010 2.493118
+- 5.427347 6.842060 0.816764
+- 6.297161 7.689052 0.119605
+- 6.531230 8.676649 0.517050
+- 6.814091 7.187011 -1.069023
+- 7.498074 7.791857 -1.664362
+- 6.482659 5.953119 -1.505101
+- 6.897660 5.575648 -2.439654
+- 5.604041 5.117355 -0.785636
+- 5.358720 4.126570 -1.168080
+- 5.083390 5.623004 0.411545
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.TRP.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 23 0 0 0 0
+-!entry.TRP.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "TRP" 1 25 1 "p" 0
+-!entry.TRP.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.TRP.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.TRP.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.TYR.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.176100
+- "HA" "H1" 0 1 131072 4 1 0.082580
+- "CB" "CT" 0 1 131072 5 6 -0.032040
+- "HB2" "HC" 0 1 131072 6 1 0.077470
+- "HB3" "HC" 0 1 131072 7 1 0.077470
+- "CG" "CA" 0 1 131072 8 6 -0.034160
+- "CD1" "CA" 0 1 131072 9 6 -0.120710
+- "HD1" "HA" 0 1 131072 10 1 0.140120
+- "CE1" "CA" 0 1 131072 11 6 -0.333900
+- "HE1" "HA" 0 1 131072 12 1 0.188970
+- "CZ" "CA" 0 1 131072 13 6 0.442780
+- "OH" "OH" 0 1 131072 14 8 -0.541860
+- "HH" "HO" 0 1 131072 15 1 0.380280
+- "CE2" "CA" 0 1 131072 16 6 -0.333900
+- "HE2" "HA" 0 1 131072 17 1 0.188970
+- "CD2" "CA" 0 1 131072 18 6 -0.120710
+- "HD2" "HA" 0 1 131072 19 1 0.140120
+- "C" "C" 0 1 131072 20 6 0.670480
+- "O" "O" 0 1 131072 21 8 -0.583250
+-!entry.TYR.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB2" "HC" 0 -1 0.0
+- "HB3" "HC" 0 -1 0.0
+- "CG" "CA" 0 -1 0.0
+- "CD1" "CA" 0 -1 0.0
+- "HD1" "HA" 0 -1 0.0
+- "CE1" "CA" 0 -1 0.0
+- "HE1" "HA" 0 -1 0.0
+- "CZ" "CA" 0 -1 0.0
+- "OH" "OH" 0 -1 0.0
+- "HH" "HO" 0 -1 0.0
+- "CE2" "CA" 0 -1 0.0
+- "HE2" "HA" 0 -1 0.0
+- "CD2" "CA" 0 -1 0.0
+- "HD2" "HA" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.TYR.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.TYR.unit.childsequence single int
+- 2
+-!entry.TYR.unit.connect array int
+- 1
+- 20
+-!entry.TYR.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 20 1
+- 5 6 1
+- 5 7 1
+- 5 8 1
+- 8 9 1
+- 8 18 1
+- 9 10 1
+- 9 11 1
+- 11 12 1
+- 11 13 1
+- 13 14 1
+- 13 16 1
+- 14 15 1
+- 16 17 1
+- 16 18 1
+- 18 19 1
+- 20 21 1
+-!entry.TYR.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+- "R" 1 "A" 17
+- "R" 1 "A" 18
+- "R" 1 "A" 19
+- "R" 1 "A" 20
+- "R" 1 "A" 21
+-!entry.TYR.unit.name single str
+- "TYR"
+-!entry.TYR.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.877484 3.115795 2.131197
+- 4.267328 4.996267 1.194946
+- 4.059927 5.918911 2.227280
+- 3.400108 5.668218 3.057877
+- 4.699998 7.163547 2.192791
+- 4.538522 7.881891 2.996538
+- 5.547471 7.485542 1.125970
+- 6.169255 8.694617 1.092468
+- 5.956327 9.246984 1.848214
+- 5.754875 6.562900 0.093635
+- 6.414694 6.813595 -0.736962
+- 5.114806 5.318263 0.128119
+- 5.276286 4.599920 -0.675627
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.TYR.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 20 0 0 0 0
+-!entry.TYR.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "TYR" 1 22 1 "p" 0
+-!entry.TYR.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.TYR.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.TYR.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+-!entry.VAL.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+- "N" "N" 0 1 131072 1 7 -0.404070
+- "H" "H" 0 1 131072 2 1 0.291460
+- "CA" "CT" 0 1 131072 3 6 -0.248670
+- "HA" "H1" 0 1 131072 4 1 0.096610
+- "CB" "CT" 0 1 131072 5 6 0.652680
+- "HB" "HC" 0 1 131072 6 1 -0.125280
+- "CG1" "CT" 0 1 131072 7 6 -0.741410
+- "HG11" "HC" 0 1 131072 8 1 0.188810
+- "HG12" "HC" 0 1 131072 9 1 0.188810
+- "HG13" "HC" 0 1 131072 10 1 0.188810
+- "CG2" "CT" 0 1 131072 11 6 -0.741410
+- "HG21" "HC" 0 1 131072 12 1 0.188810
+- "HG22" "HC" 0 1 131072 13 1 0.188810
+- "HG23" "HC" 0 1 131072 14 1 0.188810
+- "C" "C" 0 1 131072 15 6 0.670480
+- "O" "O" 0 1 131072 16 8 -0.583250
+-!entry.VAL.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+- "N" "N" 0 -1 0.0
+- "H" "H" 0 -1 0.0
+- "CA" "CT" 0 -1 0.0
+- "HA" "H1" 0 -1 0.0
+- "CB" "CT" 0 -1 0.0
+- "HB" "HC" 0 -1 0.0
+- "CG1" "CT" 0 -1 0.0
+- "HG11" "HC" 0 -1 0.0
+- "HG12" "HC" 0 -1 0.0
+- "HG13" "HC" 0 -1 0.0
+- "CG2" "CT" 0 -1 0.0
+- "HG21" "HC" 0 -1 0.0
+- "HG22" "HC" 0 -1 0.0
+- "HG23" "HC" 0 -1 0.0
+- "C" "C" 0 -1 0.0
+- "O" "O" 0 -1 0.0
+-!entry.VAL.unit.boundbox array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.VAL.unit.childsequence single int
+- 2
+-!entry.VAL.unit.connect array int
+- 1
+- 15
+-!entry.VAL.unit.connectivity table  int atom1x  int atom2x  int flags
+- 1 2 1
+- 1 3 1
+- 3 4 1
+- 3 5 1
+- 3 15 1
+- 5 6 1
+- 5 7 1
+- 5 11 1
+- 7 8 1
+- 7 9 1
+- 7 10 1
+- 11 12 1
+- 11 13 1
+- 11 14 1
+- 15 16 1
+-!entry.VAL.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+- "U" 0 "R" 1
+- "R" 1 "A" 1
+- "R" 1 "A" 2
+- "R" 1 "A" 3
+- "R" 1 "A" 4
+- "R" 1 "A" 5
+- "R" 1 "A" 6
+- "R" 1 "A" 7
+- "R" 1 "A" 8
+- "R" 1 "A" 9
+- "R" 1 "A" 10
+- "R" 1 "A" 11
+- "R" 1 "A" 12
+- "R" 1 "A" 13
+- "R" 1 "A" 14
+- "R" 1 "A" 15
+- "R" 1 "A" 16
+-!entry.VAL.unit.name single str
+- "VAL"
+-!entry.VAL.unit.positions table  dbl x  dbl y  dbl z
+- 3.325770 1.547909 -1.607204E-06
+- 3.909407 0.723611 -2.739882E-06
+- 3.970048 2.845795 -1.311163E-07
+- 3.671663 3.400129 -0.889820
+- 3.576965 3.653838 1.232143
+- 2.496995 3.801075 1.241379
+- 3.997712 2.900483 2.489542
+- 5.077693 2.753265 2.481244
+- 3.716972 3.477628 3.370558
+- 3.499630 1.931323 2.516834
+- 4.274186 5.009602 1.194577
+- 3.973781 5.548460 0.295972
+- 3.993559 5.587585 2.075079
+- 5.354271 4.863178 1.185788
+- 5.485541 2.705207 -4.398755E-06
+- 6.008824 1.593175 -8.449768E-06
+-!entry.VAL.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+- 1 15 0 0 0 0
+-!entry.VAL.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+- "VAL" 1 17 1 "p" 0
+-!entry.VAL.unit.residuesPdbSequenceNumber array int
+- 0
+-!entry.VAL.unit.solventcap array dbl
+- -1.000000
+- 0.0
+- 0.0
+- 0.0
+- 0.0
+-!entry.VAL.unit.velocities table  dbl x  dbl y  dbl z
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+- 0.0 0.0 0.0
+diff --git a/dat/leap/parm/frcmod.pol12 b/dat/leap/parm/frcmod.pol12
+deleted file mode 100644
+index cff8162..0000000
+--- a/dat/leap/parm/frcmod.pol12
++++ /dev/null
+@@ -1,180 +0,0 @@
+-Mainchain torsion parameters
+-IPOL
+-  4
+-
+-MASS
+-
+-BOND
+-
+-ANGL
+-
+-DIHEDRAL
+-C -N -CT-C    1    0.79            0.0        -1.  1.0  2.0 frm gly phi-psi gas map MP2(CBS, atz-aqz)+CCSD(T)(adz)
+-C -N -CT-C    1    1.24            0.0        -2.  1.0  2.0 frm gly phi-psi gas map MP2(CBS, atz-aqz)+CCSD(T)(adz)
+-C -N -CT-C    1    0.42            0.0         3.  1.0  2.0 frm gly phi-psi gas map MP2(CBS, atz-aqz)+CCSD(T)(adz)
+-N -CT-C -N    1    1.96            0.0        -1.  1.0  2.0 frm gly phi-psi gas map MP2(CBS, atz-aqz)+CCSD(T)(adz)
+-N -CT-C -N    1    1.37          180.0        -2.  1.0  2.0 frm gly phi-psi gas map MP2(CBS, atz-aqz)+CCSD(T)(adz)
+-N -CT-C -N    1    0.42          180.0         3.  1.0  2.0 frm gly phi-psi gas map MP2(CBS, atz-aqz)+CCSD(T)(adz)
+-CT-CT-N -C    1    0.02          180.0        -1.  1.0  2.0 
+-CT-CT-N -C    1    0.65            0.0         2.  1.0  2.0 
+-H1-CT-N -C    1    0.99          180.0        -1.  1.0  2.0 
+-H1-CT-N -C    1    0.80            0.0         2.  1.0  2.0 
+-CT-CT-C -N    1    1.34            0.0        -1.  1.0  2.0 
+-CT-CT-C -N    1    0.50          180.0         2.  1.0  2.0 
+-H1-CT-C -N    1    0.09          180.0        -2.  1.0  2.0 
+-H1-CT-C -N    1    1.14            0.0         1.  1.0  2.0 
+-
+-NONBON
+-
+-CMAP
+-%FLAG CMAP_COUNT 3
+-%FLAG CMAP_TITLE
+-ALA CMAP
+-%FLAG CMAP_RESLIST 26
+-ALA ASP SER THR LEU ILE VAL ASN GLN ARG
+-HID HIE HIP TRP PHE TYR GLU ASP LYS LYN
+-CYS CYX MET ASH GLH CYM
+-%FLAG CMAP_RESOLUTION 18
+-%FLAG CMAP_PARAMETER
+-   0.6996   0.7109   0.7452   0.8985   1.2822   1.4924   0.8283   0.0309
+-   0.1762  -0.0044  -0.9781  -0.9596  -0.2536   0.2216   0.2768   0.2998
+-   0.3343   0.4811   0.6979   0.5886   0.6524   0.9473   1.2845   1.1558
+-   0.6335   0.2926   0.8031  -0.6203  -1.0679  -0.8046  -0.1339   0.1863
+-   0.2679   0.4891   0.6519   0.7084   0.4314   0.4697   0.7114   1.0596
+-   1.0858   0.7096   0.5322   1.0603  -0.2603  -0.9325  -0.9777  -0.5784
+-  -0.1384  -0.0963   0.0316   0.3500   0.5028   0.4746   0.6188   0.9074
+-   1.1282   1.2028   0.9105   0.6231   1.0358   0.2832  -0.7467  -0.8248
+-  -0.5121  -0.1238  -0.1961  -0.4874  -0.2169   0.2218   0.4082   0.4486
+-   0.9788   1.1395   1.0923   1.0718   0.9625   1.1138   1.3863  -0.1392
+-  -0.7237  -0.2872   0.4985   0.3261  -0.5791  -1.0942  -0.4770   0.2321
+-   0.5573   0.7415   0.5292   0.4950   0.5479   0.9137   1.3146   1.8892
+-   0.9379  -0.6194  -0.6632   0.6898   1.7557   1.5728   0.6566  -0.5970
+-  -0.8672  -0.1900   0.2293   0.4321  -1.0380  -0.5799   0.3862   1.5984
+-   2.3166   2.1500  -0.0677  -1.2216   0.0062   2.3366   3.2155   2.7916
+-   1.8380   0.3829  -0.8178  -1.0808  -1.1518  -1.1570  -1.8094  -0.0773
+-   2.1498   3.7544   3.6406   0.8498  -1.3804  -0.9843   1.5549   3.2365
+-   3.3981   2.9209   2.2171   0.8749  -0.6221  -2.0341  -2.7537  -2.6330
+-  -0.3319   2.8137   3.2646   1.8770   0.3246  -1.2216  -1.4980   0.5532
+-   2.1118   2.6618   2.5746   2.5164   2.1009   0.9974  -1.3076  -2.7967
+-  -2.9532  -2.1699   3.6877   0.8028  -0.7043  -1.5370  -1.7409  -1.0954
+-   0.5853   1.2217   1.6359   1.8122   2.1382   2.1394   1.1467  -1.1553
+-  -2.0555  -1.8169  -1.0220   0.4087   0.0138  -2.0970  -3.0277  -2.8743
+-  -1.2829   0.5478   1.1379   1.4164   1.7734   2.3230   2.4142   1.2562
+-  -1.5766  -1.7018  -0.3087   1.2616   2.6633   2.9485  -1.7710  -2.9352
+-  -3.2016  -2.3880  -0.8571   0.2752   1.2115   1.6828   2.2605   2.5641
+-   1.5681  -1.1818  -2.0490  -0.0671   2.4541   3.1648   1.9621   0.0054
+-  -0.5880  -1.1331  -1.1982  -0.9946  -0.7792  -0.0902   0.9375   1.5375
+-   1.8883   1.4039  -0.3318  -1.8684  -0.9853   1.1723   2.2107   1.9406
+-   1.1240   0.2128   1.1816   0.7833   0.6454   0.3474  -0.5170  -0.9473
+-  -0.1769   0.3671   0.4441  -0.0054  -1.1102  -1.1976   0.1113   1.5763
+-   1.7120   1.7491   1.6278   1.5039   1.8743   1.3537   1.1335   0.8916
+-   0.2183  -0.9854  -1.0827  -0.5687  -0.2308  -0.5702  -0.8166  -0.2464
+-   1.0822   1.2795   1.3026   1.7406   1.9548   2.1020   1.2800   0.9715
+-   0.8172   0.7412   0.5890   0.3522   0.0954  -0.2460  -0.5892  -0.5927
+-  -0.2446   0.9237   1.1241   0.5542   1.0488   1.5582   1.5830   1.4282
+-   0.3882   0.4559   0.4963   0.4920   0.6253   0.9252   0.5006  -0.7605
+-  -0.6854  -0.3495   0.6981   0.6922  -0.0579   0.2654   0.8917   0.9409
+-   0.5017   0.1950   0.2477   0.3903   0.5167   0.6139   0.8817   1.2830
+-   0.7453  -0.3047  -0.4839   0.3175  -0.1271  -0.8020  -0.3850   0.2424
+-   0.4141   0.2357  -0.0419  -0.0473
+-%FLAG CMAP_TITLE
+-GLY CMAP
+-%FLAG CMAP_RESLIST 1
+-GLY
+-%FLAG CMAP_RESOLUTION 18
+-%COMMENT  GLY CMAP from MP2(CBS atz-aqz)+CCSD(T)(adz) correction
+-%COMMENT  from gly-CMAP-optBBV01-gas-formatted-psi-phi.dat
+-%COMMENT  PSI PHI
+-%FLAG CMAP_PARAMETER
+-   1.1507   0.7349   0.5033   0.4851   0.6055   0.6617  -0.1372  -0.4814
+-  -0.4244   3.5760  -0.4244  -0.4814  -0.1372   0.6617   0.6055   0.4851
+-   0.5033   0.7349   0.8169   0.6015   0.5487   0.7802   1.0366   0.9827
+-   0.5364   0.2725   1.1192  -0.5549  -1.1726  -0.9070  -0.1156   0.2913
+-   0.3275   0.4620   0.6558   0.7885   0.7603   0.7381   0.9566   1.2999
+-   1.3313   0.9787   0.8744   1.4168  -0.1690  -1.1676  -1.3768  -1.0856
+-  -0.2490  -0.0108   0.1378   0.4506   0.6648   0.7392   0.9915   1.1016
+-   1.2424   1.3636   1.2423   1.0643   1.4604   0.6995  -0.6354  -1.0819
+-  -0.9636  -0.5145  -0.2270  -0.2924   0.0124   0.4572   0.7197   0.8353
+-   1.1798   1.1241   1.1031   1.2584   1.3540   1.5273   1.8196   0.1895
+-  -0.6672  -0.5774  -0.0897  -0.1227  -0.6643  -0.9178  -0.3044   0.4086
+-   0.7943   1.0196   0.4751   0.3508   0.5391   1.1479   1.6817   2.1172
+-   1.0757  -0.5530  -0.7982   0.1466   0.8419   0.8318   0.3350  -0.6135
+-  -0.8554  -0.2406   0.1999   0.4241  -1.1995  -0.7114   0.4296   1.8756
+-   2.6117   2.1615  -0.1812  -1.4398  -0.4034   1.4799   2.2439   2.0908
+-   1.5528   0.3805  -0.8859  -1.3330  -1.4658  -1.4169  -1.7376   0.0374
+-   2.3126   3.9828   3.4776   0.7125  -1.5839  -1.2740   1.1103   2.4687
+-   2.5524   2.2668   1.9382   0.8766  -0.7227  -2.3671  -3.1074  -2.8081
+-   0.1638   3.0876   3.5261   1.9682   0.2306  -1.3484  -1.5582   0.5419
+-   1.8350   2.0962   1.8764   1.8112   1.6715   0.8664  -1.3883  -2.9899
+-  -3.0123  -1.9469   5.5352   1.0681  -0.6188  -1.6349  -1.9353  -1.1019
+-   0.8247   1.4255   1.5776   1.8010   1.5776   1.4255   0.8247  -1.1019
+-  -1.9353  -1.6349  -0.6188   1.0681   0.1638  -1.9469  -3.0123  -2.9899
+-  -1.3883   0.8664   1.6715   1.8112   1.8764   2.0962   1.8350   0.5419
+-  -1.5582  -1.3484   0.2306   1.9682   3.5261   3.0876  -1.7376  -2.8081
+-  -3.1074  -2.3671  -0.7227   0.8766   1.9382   2.2668   2.5524   2.4687
+-   1.1103  -1.2740  -1.5839   0.7125   3.4776   3.9828   2.3126   0.0374
+-  -1.1995  -1.4169  -1.4658  -1.3330  -0.8859   0.3805   1.5528   2.0908
+-   2.2439   1.4799  -0.4034  -1.4398  -0.1812   2.1615   2.6117   1.8756
+-   0.4296  -0.7114   0.4751   0.4241   0.1999  -0.2406  -0.8554  -0.6135
+-   0.3350   0.8318   0.8419   0.1466  -0.7982  -0.5530   1.0757   2.1172
+-   1.6817   1.1479   0.5391   0.3508   1.1798   1.0196   0.7943   0.4086
+-  -0.3044  -0.9178  -0.6643  -0.1227  -0.0897  -0.5774  -0.6672   0.1895
+-   1.8196   1.5273   1.3540   1.2584   1.1031   1.1241   0.9915   0.8353
+-   0.7197   0.4572   0.0124  -0.2924  -0.2270  -0.5145  -0.9636  -1.0819
+-  -0.6354   0.6995   1.4604   1.0643   1.2423   1.3636   1.2424   1.1016
+-   0.7603   0.7392   0.6648   0.4506   0.1378  -0.0108  -0.2490  -1.0856
+-  -1.3768  -1.1676  -0.1690   1.4168   0.8744   0.9787   1.3313   1.2999
+-   0.9566   0.7381   0.8169   0.7885   0.6558   0.4620   0.3275   0.2913
+-  -0.1156  -0.9070  -1.1726  -0.5549   1.1192   0.2725   0.5364   0.9827
+-   1.0366   0.7802   0.5487   0.6015
+-%FLAG CMAP_TITLE
+-PRO CMAP
+-%FLAG CMAP_RESLIST 1
+-PRO
+-%FLAG CMAP_RESOLUTION 18
+-%COMMENT  PRO CMAP from MP2(atz) correction
+-%COMMENT  PSI PHI
+-%FLAG CMAP_PARAMETER
+- -11.8681 -11.9836 -12.3616 -13.6168 -14.1453 -14.0496 -13.2367 -11.7198
+- -12.3096 -13.3794 -14.8656 -16.1479 -16.2807 -15.2755 -14.2653 -13.6480
+- -13.2047 -12.3285  -6.6149  -6.6085  -6.9286  -8.0418  -8.9648  -9.1397
+-  -8.0198  -7.5099  -8.3788  -9.3943 -10.1089 -10.4542 -10.0455  -9.4001
+-  -8.8431  -8.2531  -7.6409  -6.9275  -2.2957  -2.2463  -2.3664  -3.3373
+-  -4.3855  -4.6521  -3.5502  -3.0913  -3.9517  -5.7538  -5.9899  -5.5195
+-  -4.8746  -4.7226  -4.4199  -3.7774  -3.1315  -2.5488   0.6680   0.7260
+-   0.9072   0.3973  -0.5339  -0.8094   0.0774  -0.6931  -1.1404  -1.1815
+-  -1.1333  -0.6621  -0.7192  -1.4151  -1.1788  -0.0419   1.2083   0.4615
+-   2.1095   4.2916   4.4484   4.5978   2.0399   2.3643   1.5854  -0.6165
+-  -2.3163  -2.1003  -1.6863  -2.0963   1.1545   0.2034   0.3478   1.5816
+-   2.8385   3.6463   1.4654   1.9240   2.1607   2.3294   2.1657   1.1236
+-   0.0568  -1.0419  -1.1277   0.0585   1.0645   0.9305  -0.0229  -1.3432
+-  -1.8853  -0.9112   0.1465   0.8421   0.7720   0.5083   2.0895   4.2326
+-   3.4621   1.6070  -0.1446  -0.4766   0.0496   1.9172   2.8496   2.5803
+-   1.8081   0.4834  -0.8311  -0.9350  -0.4975   0.0686   0.1101   2.1266
+-   4.1675   4.8614   3.2766   0.8449  -1.0386  -0.7694   1.0610   2.6106
+-   2.9484   2.6931   2.3165   1.1273  -0.6244  -1.8051  -1.8110  -1.1012
+-   0.8389   3.2290   4.5077   3.5467   1.5644  -0.8184  -1.6190  -0.0314
+-   1.4359   1.9499   1.9228   2.1114   2.0614   0.8497  -1.6471  -2.9782
+-  -2.4091  -1.0655   2.1214   2.4093   1.8722   0.8322  -0.9802  -2.0624
+-  -0.9195  -0.7585   0.3481   0.2424   0.7417   1.3245   0.8544  -1.4936
+-  -3.4435  -3.2387  -1.8418  -0.1330   1.1045  -0.0764  -1.2071  -2.5678
+-  -3.1670  -2.1847  -1.3846  -1.6251  -1.7513  -1.1878  -0.5694  -0.9375
+-  -3.0564  -4.7386  -4.5548  -3.3367  -2.2528  -0.6426  -2.6725  -4.4937
+-  -5.8072  -6.1904  -5.2607  -4.0146  -3.6532  -3.7922  -3.4941  -3.0741
+-  -3.5874  -5.8952  -8.2189  -7.9584  -6.6024  -5.1969  -2.9854  -5.5137
+-  -7.9466  -9.1555  -9.7366  -9.4550  -8.4636  -7.2113  -6.5882  -6.3548
+-  -6.2295  -6.8226  -8.8572 -11.4670 -11.6480 -10.2777  -8.5312  -6.9800
+-  -8.2061  -5.8153 -11.6999 -12.2452 -12.6181 -13.0581 -13.3102 -12.5095
+- -11.5831 -11.1878 -11.4400 -12.4275 -14.0503 -14.7786 -14.2390 -13.2677
+- -14.5183 -11.0713 -10.6889 -11.0171 -13.0625 -13.4223 -13.6765 -14.3336
+- -14.6319 -14.0585 -16.8736 -16.1852 -15.4669 -15.8732 -16.5863 -16.5814
+- -16.0226 -15.6145 -14.9156 -14.2166 -13.6532 -13.3471 -14.4252 -14.5993
+- -14.7349 -15.6092 -15.9535 -15.6075 -16.3631 -15.6054 -15.8061 -16.5334
+- -17.0429 -16.9562 -16.5669 -16.5470 -15.8568 -15.1665 -15.5102 -15.0609
+- -15.7879 -15.7763 -15.7932 -16.8848 -17.2752 -17.1565 -17.2433 -16.5548
+- -16.1162 -16.6112 -17.8811 -19.0447 -19.4487 -18.9047 -17.8098 -17.1771
+- -17.3673 -16.7746 -17.1505 -16.9534 -16.8516 -18.1603 -18.1481 -18.1358
+- -18.1236 -17.5042 -16.4263 -16.6890 -18.7194 -21.1332 -22.3304 -21.2623
+- -19.7629 -19.1877 -19.2243 -18.4884
+-
+-
+diff --git a/dat/leap/parm/parmpol12.dat b/dat/leap/parm/parmpol12.dat
+deleted file mode 100644
+index 13fefad..0000000
+--- a/dat/leap/parm/parmpol12.dat
++++ /dev/null
+@@ -1,756 +0,0 @@
+-based on PARM99 ff11D1, Thole-Linear SL=2.5874
+-C  12.01         1.2955    2.5874    sp2 C carbonyl group 
+-C2 12.01         1.2955    2.5874    sp2 C
+-CA 12.01         1.2955    2.5874    sp2 C pure aromatic (benzene)
+-CB 12.01         1.2955    2.5874    sp2 aromatic C, 5&6 membered ring junction
+-CC 12.01         1.2955    2.5874    sp2 aromatic C, 5 memb. ring HIS
+-CD 12.01         1.2955    2.5874    sp2 C atom in the middle of: C=CD-CD=C
+-CK 12.01         1.2955    2.5874    sp2 C 5 memb.ring in purines
+-CM 12.01         1.2955    2.5874    sp2 C  pyrimidines in pos. 5 & 6
+-CN 12.01         1.2955    2.5874    sp2 C aromatic 5&6 memb.ring junct.(TRP)
+-CQ 12.01         1.2955    2.5874    sp2 C in 5 mem.ring of purines between 2 N
+-CR 12.01         1.2955    2.5874    sp2 arom as CQ but in HIS
+-CT 12.01         0.9399    2.5874    sp3 aliphatic C
+-CV 12.01         1.2955    2.5874    sp2 arom. 5 memb.ring w/1 N and 1 H (HIS)
+-CW 12.01         1.2955    2.5874    sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS)
+-C* 12.01         1.2955    2.5874    sp2 arom. 5 memb.ring w/1 subst. (TRP)
+-CY 12.01         1.3916    2.5874    nitrile C (Howard et al.JCC,16,243,1995)
+-CZ 12.01         1.3916    2.5874    sp C (Howard et al.JCC,16,243,1995)
+-C0 40.08                               calcium
+-H  1.008         0.4255    2.5874    H bonded to nitrogen atoms
+-H0 1.008         0.4255    2.5874    for Gly only
+-HC 1.008         0.4255    2.5874    H aliph. bond. to C without electrwd.group
+-H1 1.008         0.4255    2.5874    H aliph. bond. to C with 1 electrwd. group
+-H2 1.008         0.4255    2.5874    H aliph. bond. to C with 2 electrwd.groups
+-H3 1.008         0.4255    2.5874    H aliph. bond. to C with 3 eletrwd.groups
+-HA 1.008         0.4255    2.5874    H arom. bond. to C without elctrwd. groups
+-H4 1.008         0.4255    2.5874    H arom. bond. to C with 1 electrwd. group
+-H5 1.008         0.4255    2.5874    H arom.at C with 2 elctrwd. gr,+HCOO group
+-HO 1.008         0.4255    2.5874    hydroxyl group
+-HS 1.008         0.4255    2.5874    hydrogen bonded to sulphur (pol?)
+-HW 1.008         0.1700    2.4410    H in POL3 water
+-HP 1.008         0.4255    2.5874    H bonded to C next to positively charged gr
+-HZ 1.008         0.4255    2.5874    H bond sp C (Howard et al.JCC,16,243,1995)
+-F  19.00         0.4839    2.5874    fluorine
+-Cl 35.45         2.3707    2.5874    chlorine
+-IM 35.45         2.3707    2.5874    assumed to be Cl- (ion minus)
+-Br 79.90         3.5016    2.5874    bromine
+-I  126.9         5.5787    2.5874    iodine
+-IB 131.0                             'big ion w/ waters' for vacuum (Na+, 6H2O)
+-MG 24.305        0.120     2.5874     magnesium
+-N  14.01         0.9603    2.5874    sp2 nitrogen in amide groups
+-NA 14.01         0.9603    2.5874    sp2 N in 5 memb.ring w/H atom (HIS)
+-NB 14.01         0.9603    2.5874    sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
+-NC 14.01         0.9603    2.5874    sp2 N in 6 memb.ring w/LP (ADE,GUA)
+-N2 14.01         0.9603    2.5874    sp2 N in amino groups
+-N3 14.01         0.9603    2.5874    sp3 N for charged amino groups (Lys, etc)
+-NT 14.01         0.9603    2.5874    sp3 N for amino groups amino groups 
+-N* 14.01         0.9603    2.5874    sp2 N 
+-NY 14.01         0.9603    2.5874    nitrile N (Howard et al.JCC,16,243,1995)
+-O  16.00         0.6049    2.5874    carbonyl group oxygen
+-O2 16.00         0.6049    2.5874    carboxyl and phosphate group oxygen
+-OW 16.00         0.5280    2.4410    oxygen in POL3 water
+-OH 16.00         0.6148    2.5874    oxygen in hydroxyl group
+-OS 16.00         0.6148    2.5874    ether and ester oxygen
+-P  30.97         1.7927    2.5874    phosphate,pol:JACS,112,8543,90,K.J.Miller
+-S  32.06         3.1686    2.5874    S in disulfide linkage,pol:JPC,102,2399,98
+-SH 32.06         3.1686    2.5874    S in cystine
+-S4 32.06         2.3149    2.5874    S
+-CU 63.55                             copper
+-FE 55.00                             iron
+-Li  6.94         0.029     2.5874    lithium, ions pol:J.PhysC,11,1541,(1978)
+-IP 22.99         0.250     2.5874    assumed to be Na+ (ion plus)
+-Na 22.99         0.250     2.5874    Na+, ions pol:J.PhysC,11,1541,(1978)
+-K  39.10         1.060     2.5874    potassium
+-Rb 85.47                             rubidium
+-Cs 132.91                            cesium
+-Zn  65.4                             Zn2+ 
+-LP  3.00         0.000               lone pair
+-
+-C   H   HO  N   NA  NB  NC  N2  NT  N2  N3  N*  O   OH  OS  P   O2 
+-OW-HW  320.0    1.0000    ! POL3, SPC/E water
+-HW-HW  553.0    1.6330      POL3, SPC/E water
+-C -C   310.0    1.525       Junmei et al, 1999
+-C -CA  469.0    1.409       JCC,7,(1986),230; (not used any more in TYR)
+-C -CB  447.0    1.419       JCC,7,(1986),230; GUA
+-C -CM  410.0    1.444       JCC,7,(1986),230; THY,URA
+-C -CT  317.0    1.522       JCC,7,(1986),230; AA
+-C -N   490.0    1.335       JCC,7,(1986),230; AA
+-C -N*  424.0    1.383       JCC,7,(1986),230; CYT,URA
+-C -NA  418.0    1.388       JCC,7,(1986),230; GUA.URA
+-C -NC  457.0    1.358       JCC,7,(1986),230; CYT
+-C -O   570.0    1.229       JCC,7,(1986),230; AA,CYT,GUA,THY,URA
+-C -O2  656.0    1.250       JCC,7,(1986),230; GLU,ASP
+-C -OH  450.0    1.364       JCC,7,(1986),230; (not used any more for TYR) 
+-C -OS  450.0    1.323       Junmei et al, 1999
+-C -H4  367.0    1.080       Junmei et al, 1999
+-C -H5  367.0    1.080       Junmei et al, 1999
+-CA-CA  469.0    1.400       JCC,7,(1986),230; BENZENE,PHE,TRP,TYR
+-CA-CB  469.0    1.404       JCC,7,(1986),230; ADE,TRP
+-CA-CM  427.0    1.433       JCC,7,(1986),230; CYT
+-CA-CN  469.0    1.400       JCC,7,(1986),230; TRP
+-CA-CT  317.0    1.510       JCC,7,(1986),230; PHE,TYR
+-CA-HA  367.0    1.080       changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR
+-CA-H4  367.0    1.080       changed from 340. bsd on C6H6 nmodes; no assigned
+-CA-N2  481.0    1.340       JCC,7,(1986),230; ARG,CYT,GUA
+-CA-NA  427.0    1.381       JCC,7,(1986),230; GUA
+-CA-NC  483.0    1.339       JCC,7,(1986),230; ADE,CYT,GUA
+-CA-OH  450.0    1.364       substituted for C-OH in tyr 
+-CB-CB  520.0    1.370       JCC,7,(1986),230; ADE,GUA
+-CB-N*  436.0    1.374       JCC,7,(1986),230; ADE,GUA
+-CB-NB  414.0    1.391       JCC,7,(1986),230; ADE,GUA
+-CB-NC  461.0    1.354       JCC,7,(1986),230; ADE,GUA
+-CD-HA  367.0    1.080       Junmei et al, 1999 
+-CD-CD  469.0    1.400       Junmei et al, 1999
+-CD-CM  549.0    1.350       Junmei et al, 1999
+-CD-CT  317.0    1.510       Junmei et al, 1999
+-CK-H5  367.0    1.080       changed from 340. bsd on C6H6 nmodes; ADE,GUA
+-CK-N*  440.0    1.371       JCC,7,(1986),230; ADE,GUA
+-CK-NB  529.0    1.304       JCC,7,(1986),230; ADE,GUA
+-CM-CM  549.0    1.350       JCC,7,(1986),230; CYT,THY,URA
+-CM-CT  317.0    1.510       JCC,7,(1986),230; THY
+-CM-HA  367.0    1.080       changed from 340. bsd on C6H6 nmodes; CYT,URA
+-CM-H4  367.0    1.080       changed from 340. bsd on C6H6 nmodes; CYT,URA
+-CM-H5  367.0    1.080       changed from 340. bsd on C6H6 nmodes; not assigned
+-CM-N*  448.0    1.365       JCC,7,(1986),230; CYT,THY,URA
+-CM-OS  480.0    1.240       Junmei et al, 1999
+-CQ-H5  367.0    1.080       changed from 340. bsd on C6H6 nmodes; ADE
+-CQ-NC  502.0    1.324       JCC,7,(1986),230; ADE
+-CT-CT  310.0    1.526       JCC,7,(1986),230; AA, SUGARS
+-CT-HC  340.0    1.090       changed from 331 bsd on NMA nmodes; AA, SUGARS
+-CT-H0  340.0    1.090       changed from 331 bsd on NMA nmodes; AA, RIBOSE
+-CT-H1  340.0    1.090       changed from 331 bsd on NMA nmodes; AA, RIBOSE
+-CT-H2  340.0    1.090       changed from 331 bsd on NMA nmodes; SUGARS
+-CT-H3  340.0    1.090       changed from 331 bsd on NMA nmodes; not assigned
+-CT-HP  340.0    1.090       changed from 331; AA-lysine, methyl ammonium cation
+-CT-N*  337.0    1.475       JCC,7,(1986),230; ADE,CYT,GUA,THY,URA
+-CT-N2  337.0    1.463       JCC,7,(1986),230; ARG
+-CT-OH  320.0    1.410       JCC,7,(1986),230; SUGARS
+-CT-OS  320.0    1.410       JCC,7,(1986),230; NUCLEIC ACIDS
+-C*-HC  367.0    1.080       changed from 340. bsd on C6H6 nmodes, not needed AA
+-C*-CB  388.0    1.459       JCC,7,(1986),230; TRP
+-C*-CT  317.0    1.495       JCC,7,(1986),230; TRP
+-C*-CW  546.0    1.352       JCC,7,(1986),230; TRP
+-CB-CN  447.0    1.419       JCC,7,(1986),230; TRP
+-CC-CT  317.0    1.504       JCC,7,(1986),230; HIS
+-CC-CV  512.0    1.375       JCC,7,(1986),230; HIS(delta)
+-CC-CW  518.0    1.371       JCC,7,(1986),230; HIS(epsilon)
+-CC-NA  422.0    1.385       JCC,7,(1986),230; HIS
+-CC-NB  410.0    1.394       JCC,7,(1986),230; HIS
+-CN-NA  428.0    1.380       JCC,7,(1986),230; TRP
+-CR-H5  367.0    1.080       changed from 340. bsd on C6H6 nmodes;HIS
+-CR-NA  477.0    1.343       JCC,7,(1986),230; HIS
+-CR-NB  488.0    1.335       JCC,7,(1986),230; HIS
+-CT-N   337.0    1.449       JCC,7,(1986),230; AA
+-CT-N3  367.0    1.471       JCC,7,(1986),230; LYS
+-CT-NT  367.0    1.471       for neutral amines 
+-CT-S   227.0    1.810       changed from 222.0 based on dimethylS nmodes
+-CT-SH  237.0    1.810       changed from 222.0 based on methanethiol nmodes
+-CT-CY  400.0    1.458       Howard et al JCC.16,243,1995
+-CT-CZ  400.0    1.459       Howard et al JCC,16,243,1995
+-CV-H4  367.0    1.080       changed from 340. bsd on C6H6 nmodes; HIS
+-CV-NB  410.0    1.394       JCC,7,(1986),230; HIS
+-CW-H4  367.0    1.080       changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+)
+-CW-NA  427.0    1.381       JCC,7,(1986),230; HIS,TRP
+-CY-NY  600.0    1.150       Howard et al JCC,16,243,1995
+-CZ-CZ  600.0    1.206       Howard et al JCC,16,243,1995
+-CZ-HZ  400.0    1.056       Howard et al JCC,16,243,1995
+-O2-P   525.0    1.480       JCC,7,(1986),230; NA PHOSPHATES
+-OH-P   230.0    1.610       JCC,7,(1986),230; NA PHOSPHATES
+-OS-P   230.0    1.610       JCC,7,(1986),230; NA PHOSPHATES
+-H -N2  434.0    1.010       JCC,7,(1986),230; ADE,CYT,GUA,ARG
+-H -N*  434.0    1.010       for plain unmethylated bases ADE,CYT,GUA,ARG
+-H -NA  434.0    1.010       JCC,7,(1986),230; GUA,URA,HIS
+-H -N   434.0    1.010       JCC,7,(1986),230; AA
+-H -N3  434.0    1.010       JCC,7,(1986),230; LYS    
+-H -NT  434.0    1.010       for neutral amines 
+-HO-OH  553.0    0.960       JCC,7,(1986),230; SUGARS,SER,TYR
+-HO-OS  553.0    0.960       JCC,7,(1986),230; NUCLEOTIDE ENDS
+-HS-SH  274.0    1.336       JCC,7,(1986),230; CYS
+-S -S   166.0    2.038       JCC,7,(1986),230; CYX   (SCHERAGA)
+-F -CT  367.0    1.380       JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3
+-Cl-CT  232.0    1.766       6-31g* opt
+-Br-CT  159.0    1.944       Junmei et al,99 
+-I -CT  148.0    2.166       Junmei et al,99 
+-F -CA  386.0    1.359       Junmei et al,99 
+-Cl-CA  193.0    1.727       Junmei et al,99 
+-I -CA  171.0    2.075       Junmei et al,99 
+-Br-CA  172.0    1.890       Junmei et al,99
+-LP-O   600.0    0.200       or 0.35
+-LP-OH  600.0    0.200       or 0.35
+-LP-OS  600.0    0.200       or 0.35
+-LP-N3  600.0    0.200       or 0.35
+-LP-NT  600.0    0.200       or 0.35
+-LP-NB  600.0    0.200       or 0.35 histidines, nucleic acids
+-LP-NC  600.0    0.200       or 0.35 nucleic acids
+-LP-S   600.0    0.700       cys,cyx,met
+-LP-SH  600.0    0.700       cys,cyx
+-
+-HW-OW-HW    100.      104.52    TIP3P water
+-HW-HW-OW      0.      127.74    (found in crystallographic water with 3 bonds)
+-C -C -O     80.0      120.00    Junmei et al, 1999 acrolein
+-C -C -OH    80.0      120.00    Junmei et al, 1999
+-CA-C -CA    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes; AA
+-CA-C -OH    70.0      120.00    AA (not used in tyr)
+-CB-C -NA    70.0      111.30    NA
+-CB-C -O     80.0      128.80
+-CM-C -NA    70.0      114.10
+-CM-C -O     80.0      125.30
+-CT-C -O     80.0      120.40
+-CT-C -O2    70.0      117.00
+-CT-C -N     70.0      116.60    AA general
+-CT-C -CT    63.0      117.00    Junmei et al, 1999
+-CT-C -OS    80.0      115.00    Junmei et al, 1999
+-CT-C -OH    80.0      110.00    Junmei et al, 1999
+-N*-C -NA    70.0      115.40
+-N*-C -NC    70.0      118.60
+-N*-C -O     80.0      120.90
+-NA-C -O     80.0      120.60
+-NC-C -O     80.0      122.50
+-N -C -O     80.0      122.90    AA general
+-O -C -O     80.0      126.00    AA COO- terminal residues
+-O -C -OH    80.0      120.00    (check with Junmei for: theta0:120.0?)
+-O -C -OS    80.0      125.00    Junmei et al, 1999
+-O2-C -O2    80.0      126.00    AA GLU            (SCH JPC 79,2379)
+-H4-C -C     50.0      120.00    Junmei et al, 1999 
+-H4-C -CM    50.0      115.00    Junmei et al, 1999 
+-H4-C -CT    50.0      115.00    Junmei et al, 1999
+-H4-C -O     50.0      120.00    Junmei et al, 1999
+-H4-C -OH    50.0      120.00    Junmei et al, 1999
+-H5-C -N     50.0      120.00    Junmei et al, 1999
+-H5-C -O     50.0      119.00    Junmei et al, 1999
+-H5-C -OH    50.0      107.00    Junmei et al, 1999
+-H5-C -OS    50.0      107.00    Junmei et al, 1999
+-C -CA-CA    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes
+-C -CA-HA    50.0      120.00    AA (not used in tyr)
+-CA-CA-CA    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes
+-CA-CA-CB    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes
+-CA-CA-CT    70.0      120.00
+-CA-CA-HA    50.0      120.00
+-CA-CA-H4    50.0      120.00
+-CA-CA-OH    70.0      120.00    replacement in tyr
+-CA-CA-CN    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes; AA trp
+-CB-CA-HA    50.0      120.00
+-CB-CA-H4    50.0      120.00
+-CB-CA-N2    70.0      123.50
+-CB-CA-NC    70.0      117.30
+-CM-CA-N2    70.0      120.10
+-CM-CA-NC    70.0      121.50
+-CN-CA-HA    50.0      120.00    AA trp
+-NA-CA-NC    70.0      123.30
+-N2-CA-NA    70.0      116.00
+-N2-CA-NC    70.0      119.30
+-N2-CA-N2    70.0      120.00    AA arg
+-F -CA-CA    70.0      121.00    Junmei et al,99 
+-Cl-CA-CA    70.0      118.80    Junmei et al,99 
+-Br-CA-CA    70.0      118.80    Junmei et al,99
+-I -CA-CA    70.0      118.80    Junmei et al,99 
+-C -CB-CB    63.0      119.20    changed from 85.0  bsd on C6H6 nmodes; NA gua
+-C -CB-NB    70.0      130.00
+-CA-CB-CB    63.0      117.30    changed from 85.0  bsd on C6H6 nmodes; NA ade
+-CA-CB-NB    70.0      132.40    
+-CB-CB-N*    70.0      106.20
+-CB-CB-NB    70.0      110.40
+-CB-CB-NC    70.0      127.70
+-C*-CB-CA    63.0      134.90    changed from 85.0  bsd on C6H6 nmodes; AA trp
+-C*-CB-CN    63.0      108.80    changed from 85.0  bsd on C6H6 nmodes; AA trp
+-CA-CB-CN    63.0      116.20    changed from 85.0  bsd on C6H6 nmodes; AA trp
+-N*-CB-NC    70.0      126.20
+-CD-CD-CM    63.0      120.00    Junmei et al, 1999
+-CD-CD-CT    70.0      120.00    Junmei et al, 1999
+-CM-CD-CT    70.0      120.00    Junmei et al, 1999
+-HA-CD-HA    35.0      119.00    Junmei et al, 1999
+-HA-CD-CD    50.0      120.00    Junmei et al, 1999
+-HA-CD-CM    50.0      120.00    Junmei et al, 1999
+-H5-CK-N*    50.0      123.05
+-H5-CK-NB    50.0      123.05
+-N*-CK-NB    70.0      113.90
+-C -CM-CM    63.0      120.70    changed from 85.0  bsd on C6H6 nmodes; NA thy
+-C -CM-CT    70.0      119.70
+-C -CM-HA    50.0      119.70
+-C -CM-H4    50.0      119.70
+-CA-CM-CM    63.0      117.00    changed from 85.0  bsd on C6H6 nmodes; NA cyt
+-CA-CM-HA    50.0      123.30
+-CA-CM-H4    50.0      123.30
+-CM-CM-CT    70.0      119.70
+-CM-CM-HA    50.0      119.70
+-CM-CM-H4    50.0      119.70
+-CM-CM-N*    70.0      121.20
+-CM-CM-OS    80.0      125.00    Junmei et al, 1999
+-H4-CM-N*    50.0      119.10
+-H4-CM-OS    50.0      113.00    Junmei et al, 1999
+-HA-CM-HA    35.0      120.00    Junmei et al, 1999
+-HA-CM-CD    50.0      120.00    Junmei et al, 1999
+-HA-CM-CT    50.0      120.00    Junmei et al, 1999
+-NC-CQ-NC    70.0      129.10
+-H5-CQ-NC    50.0      115.45
+-H0-CT-H0    35.0      109.50
+-H0-CT-N     50.0      109.50    AA general  changed based on NMA nmodes
+-C -CT-H0    50.0      109.50    AA general  changed based on NMA nmodes
+-H1-CT-H1    35.0      109.50
+-H1-CT-N*    50.0      109.50    changed based on NMA nmodes
+-H1-CT-OH    50.0      109.50    changed based on NMA nmodes 
+-H1-CT-OS    50.0      109.50    changed based on NMA nmodes 
+-H1-CT-CM    50.0      109.50    Junmei et al, 1999 
+-H1-CT-CY    50.0      110.00    Junmei et al, 1999
+-H1-CT-CZ    50.0      110.00    Junmei et al, 1999
+-H1-CT-N     50.0      109.50    AA general  changed based on NMA nmodes
+-H1-CT-S     50.0      109.50    AA cys     changed based on NMA nmodes
+-H1-CT-SH    50.0      109.50    AA cyx     changed based on NMA nmodes
+-H1-CT-N2    50.0      109.50    AA arg     changed based on NMA nmodes
+-H1-CT-NT    50.0      109.50    neutral amines 
+-H2-CT-H2    35.0      109.50    AA lys
+-H2-CT-N*    50.0      109.50    changed based on NMA nmodes
+-H2-CT-OS    50.0      109.50    changed based on NMA nmodes
+-HP-CT-HP    35.0      109.50    AA lys, ch3nh4+
+-HP-CT-N3    50.0      109.50    AA lys, ch3nh3+, changed based on NMA nmodes
+-HC-CT-HC    35.0      109.50
+-HC-CT-CM    50.0      109.50    changed based on NMA nmodes
+-HC-CT-CD    50.0      109.50    Junmei et al, 1999
+-HC-CT-CZ    50.0      110.00    Junmei et al, 1999
+-C -CT-H1    50.0      109.50    AA general  changed based on NMA nmodes
+-C -CT-HP    50.0      109.50    AA zwitterion  changed based on NMA nmodes
+-C -CT-HC    50.0      109.50    AA gln      changed based on NMA nmodes
+-C -CT-N     63.0      110.10    AA general
+-C -CT-N3    80.0      111.20    AA amino terminal residues
+-C -CT-CT    63.0      111.10    AA general
+-C -CT-OS    60.0      109.50    Junmei et al, 1999
+-CA-CT-HC    50.0      109.50    AA tyr     changed based on NMA nmodes
+-CC-CT-CT    63.0      113.10    AA his
+-CC-CT-HC    50.0      109.50    AA his     changed based on NMA nmodes
+-CM-CT-CT    63.0      111.00    Junmei et al, 1999 (last change: Mar24,99)
+-CM-CT-OS    50.0      109.50    Junmei et al, 1999
+-CT-CT-CT    40.0      109.50
+-CT-CT-HC    50.0      109.50    changed based on NMA nmodes
+-CT-CT-H1    50.0      109.50    changed based on NMA nmodes
+-CT-CT-H2    50.0      109.50    changed based on NMA nmodes
+-CT-CT-HP    50.0      109.50    changed based on NMA nmodes
+-CT-CT-N*    50.0      109.50
+-CT-CT-OH    50.0      109.50
+-CT-CT-OS    50.0      109.50
+-CT-CT-S     50.0      114.70    AA cyx            (SCHERAGA  JPC 79,1428)
+-CT-CT-SH    50.0      108.60    AA cys
+-CT-CT-CA    63.0      114.00    AA phe tyr          (SCH JPC  79,2379)
+-CT-CT-N2    80.0      111.20    AA arg             (JCP 76, 1439)
+-CT-CT-N     80.0      109.70    AA ala, general    (JACS 94, 2657)
+-CT-CT-N3    80.0      111.20    AA lys             (JCP 76, 1439)
+-CT-CT-NT    80.0      111.20    neutral amines 
+-CT-CT-CY    63.0      110.00    Junmei et al, 1999    
+-CT-CT-CZ    63.0      110.00    Junmei et al, 1999
+-C*-CT-CT    63.0      115.60    AA trp
+-C*-CT-HC    50.0      109.50    AA trp    changed based on NMA nmodes
+-OS-CT-OS   160.0      101.00    Junmei et al, 1999
+-OS-CT-CY    50.0      110.00    Junmei et al, 1999
+-OS-CT-CZ    50.0      110.00    Junmei et al, 1999
+-OS-CT-N*    50.0      109.50
+-F -CT-F     77.0      109.10    JCC,13,(1992),963;
+-F -CT-H1    50.0      109.50    JCC,13,(1992),963;
+-F -CT-CT    50.0      109.00    
+-F -CT-H2    50.0      109.50  
+-Cl-CT-CT    50.0      108.50    (6-31g* opt value)
+-Cl-CT-H1    50.0      108.50    (6-31g* opt value)  
+-Br-CT-CT    50.0      108.00    Junmei et al 99 
+-Br-CT-H1    50.0      106.50    Junmei et al 99 
+-I -CT-CT    50.0      106.00    Junmei et al,99 
+-CT-CC-NA    70.0      120.00    AA his
+-CT-CC-CV    70.0      120.00    AA his
+-CT-CC-NB    70.0      120.00    AA his
+-CV-CC-NA    70.0      120.00    AA his
+-CW-CC-NA    70.0      120.00    AA his
+-CW-CC-NB    70.0      120.00    AA his
+-CT-CC-CW    70.0      120.00    AA his
+-H5-CR-NA    50.0      120.00    AA his
+-H5-CR-NB    50.0      120.00    AA his
+-NA-CR-NA    70.0      120.00    AA his
+-NA-CR-NB    70.0      120.00    AA his
+-CC-CV-H4    50.0      120.00    AA his
+-CC-CV-NB    70.0      120.00    AA his
+-H4-CV-NB    50.0      120.00    AA his
+-CC-CW-H4    50.0      120.00    AA his
+-CC-CW-NA    70.0      120.00    AA his
+-C*-CW-H4    50.0      120.00    AA trp
+-C*-CW-NA    70.0      108.70    AA trp
+-H4-CW-NA    50.0      120.00    AA his
+-CB-C*-CT    70.0      128.60    AA trp
+-CB-C*-CW    63.0      106.40    changed from 85.0  bsd on C6H6 nmodes; AA trp
+-CT-C*-CW    70.0      125.00    AA trp
+-CA-CN-CB    63.0      122.70    changed from 85.0  bsd on C6H6 nmodes; AA trp
+-CA-CN-NA    70.0      132.80    AA trp
+-CB-CN-NA    70.0      104.40    AA trp
+-CT-CY-NY    80.0      180.00    Junmei et al, 1999
+-CT-CZ-CZ    80.0      180.00    Junmei et al, 1999
+-CZ-CZ-HZ    50.0      180.00    Junmei et al, 1999
+-C -N -CT    50.0      121.90    AA general
+-C -N -H     50.0      120.00    AA general, gln, asn,changed based on NMA nmodes
+-CT-N -H     50.0      118.04    AA general,     changed based on NMA nmodes
+-CT-N -CT    50.0      118.00    AA pro             (DETAR JACS 99,1232)
+-H -N -H     35.0      120.00    ade,cyt,gua,gln,asn     **
+-C -N*-CM    70.0      121.60
+-C -N*-CT    70.0      117.60
+-C -N*-H     50.0      119.20    changed based on NMA nmodes
+-CB-N*-CK    70.0      105.40
+-CB-N*-CT    70.0      125.80
+-CB-N*-H     50.0      125.80    for unmethylated n.a. bases,chngd bsd NMA nmodes
+-CK-N*-CT    70.0      128.80
+-CK-N*-H     50.0      128.80    for unmethylated n.a. bases,chngd bsd NMA nmodes
+-CM-N*-CT    70.0      121.20
+-CM-N*-H     50.0      121.20    for unmethylated n.a. bases,chngd bsd NMA nmodes
+-CA-N2-H     50.0      120.00    
+-CA-N2-CT    50.0      123.20    AA arg
+-CT-N2-H     50.0      118.40    AA arg
+-H -N2-H     35.0      120.00    
+-CT-N3-H     50.0      109.50    AA lys,     changed based on NMA nmodes
+-CT-N3-CT    50.0      109.50    AA pro/nt
+-H -N3-H     35.0      109.50    AA lys, AA(end)
+-CT-NT-H     50.0      109.50    neutral amines 
+-CT-NT-CT    50.0      109.50    neutral amines 
+-H -NT-H     35.0      109.50    neutral amines 
+-C -NA-C     70.0      126.40
+-C -NA-CA    70.0      125.20
+-C -NA-H     50.0      116.80    changed based on NMA nmodes
+-CA-NA-H     50.0      118.00    changed based on NMA nmodes
+-CC-NA-CR    70.0      120.00    AA his
+-CC-NA-H     50.0      120.00    AA his,    changed based on NMA nmodes
+-CR-NA-CW    70.0      120.00    AA his
+-CR-NA-H     50.0      120.00    AA his,    changed based on NMA nmodes
+-CW-NA-H     50.0      120.00    AA his,    changed based on NMA nmodes
+-CN-NA-CW    70.0      111.60    AA trp
+-CN-NA-H     50.0      123.10    AA trp,    changed based on NMA nmodes
+-CB-NB-CK    70.0      103.80
+-CC-NB-CR    70.0      117.00    AA his
+-CR-NB-CV    70.0      117.00    AA his
+-C -NC-CA    70.0      120.50
+-CA-NC-CB    70.0      112.20
+-CA-NC-CQ    70.0      118.60
+-CB-NC-CQ    70.0      111.00
+-C -OH-HO    50.0      113.00    (not used in tyr anymore)
+-CA-OH-HO    50.0      113.00    replacement in tyr
+-CT-OH-HO    55.0      108.50
+-HO-OH-P     45.0      108.50
+-C -OS-CT    60.0      117.00    Junmei et al, 1999
+-CM-OS-CT    60.0      117.00    Junmei et al, 1999
+-CT-OS-CT    60.0      109.50
+-CT-OS-P    100.0      120.50
+-P -OS-P    100.0      120.50
+-O2-P -OH    45.0      108.23
+-O2-P -O2   140.0      119.90
+-O2-P -OS   100.0      108.23
+-OH-P -OS    45.0      102.60
+-OS-P -OS    45.0      102.60
+-CT-S -CT    62.0       98.90    AA met
+-CT-S -S     68.0      103.70    AA cyx             (SCHERAGA  JPC 79,1428)
+-CT-SH-HS    43.0       96.00    changed from 44.0 based on methanethiol nmodes
+-HS-SH-HS    35.0       92.07    AA cys
+-CB-NB-LP   150.0       126.0    NA
+-CC-NB-LP   150.0       126.0    his,NA
+-CK-NB-LP   150.0       126.0    NA
+-CR-NB-LP   150.0       126.0    his,NA
+-CV-NB-LP   150.0       126.0    his,NA
+-C -NC-LP   150.0       120.0    NA
+-CA-NC-LP   150.0       120.0    NA
+-CB-NC-LP   150.0       120.0    NA
+-CQ-NC-LP   150.0       120.0    NA
+-CT-N3-LP   150.0       109.5    in neutral lysine
+-H -N3-LP   150.0       109.5    in neutral lysine
+-CT-NT-LP   150.0       109.5
+-H -NT-LP   150.0       109.5
+-C -O -LP   150.0       120.0
+-LP-O -LP   150.0       120.0
+-C -OH-LP   150.0       120.0
+-CT-OH-LP   150.0       109.5
+-HO-OH-LP   150.0       109.5
+-LP-OH-LP   150.0       109.5
+-C -OS-LP   150.0       109.5 
+-CM-OS-LP   150.0       109.5    methyl vinyl ether
+-CT-OS-LP   150.0       109.5
+-LP-OS-LP   150.0       109.5
+-CT-S -LP   150.0        90.0    cys,cyx,met
+-CT-SH-LP   150.0        90.0    cys,cyx,met
+-P -OS-LP   150.0       109.5    NA
+-LP-S -LP   150.0       180.0    cys,cyx,met
+-LP-SH-LP   150.0       180.0    cys,cyx,met
+-HS-SH-LP   150.0        90.0    cys  
+-
+-X -C -C -X    4   14.50        180.0     2.         Junmei et al, 1999
+-X -C -CA-X    4   14.50        180.0     2.         intrpol.bsd.on C6H6
+-X -C -CB-X    4   12.00        180.0     2.         intrpol.bsd.on C6H6
+-X -C -CM-X    4    8.70        180.0     2.         intrpol.bsd.on C6H6
+-X -C -CT-X    6    0.00          0.0     2.         JCC,7,(1986),230
+-X -C -N -X    4   10.00        180.0     2.         AA,NMA
+-X -C -N*-X    4    5.80        180.0     2.         JCC,7,(1986),230
+-X -C -NA-X    4    5.40        180.0     2.         JCC,7,(1986),230
+-X -C -NC-X    2    8.00        180.0     2.         JCC,7,(1986),230
+-X -C -O -X    4   11.20        180.0     2.         Junmei et al, 1999
+-X -C -OH-X    2    4.60        180.0     2.         Junmei et al, 1999
+-X -C -OS-X    2    5.40        180.0     2.         Junmei et al, 1999
+-X -CA-CA-X    4   14.50        180.0     2.         intrpol.bsd.on C6H6
+-X -CA-CB-X    4   14.00        180.0     2.         intrpol.bsd.on C6H6
+-X -CA-CM-X    4   10.20        180.0     2.         intrpol.bsd.on C6H6
+-X -CA-CN-X    4   14.50        180.0     2.         reinterpolated 93'
+-X -CA-CT-X    6    0.00          0.0     2.         JCC,7,(1986),230
+-X -CA-N2-X    4    9.60        180.0     2.         reinterpolated 93'
+-X -CA-NA-X    4    6.00        180.0     2.         JCC,7,(1986),230
+-X -CA-NC-X    2    9.60        180.0     2.         JCC,7,(1986),230
+-X -CA-OH-X    2    1.80        180.0     2.         Junmei et al, 99
+-X -CB-CB-X    4   21.80        180.0     2.         intrpol.bsd.on C6H6
+-X -CB-CN-X    4   12.00        180.0     2.         reinterpolated 93'
+-X -CB-N*-X    4    6.60        180.0     2.         JCC,7,(1986),230
+-X -CB-NB-X    2    5.10        180.0     2.         JCC,7,(1986),230
+-X -CB-NC-X    2    8.30        180.0     2.         JCC,7,(1986),230
+-X -CC-CT-X    6    0.00          0.0     2.         JCC,7,(1986),230
+-X -CC-CV-X    4   20.60        180.0     2.         intrpol.bsd.on C6H6
+-X -CC-CW-X    4   21.50        180.0     2.         intrpol.bsd.on C6H6
+-X -CC-NA-X    4    5.60        180.0     2.         JCC,7,(1986),230
+-X -CC-NB-X    2    4.80        180.0     2.         JCC,7,(1986),230
+-X -CD-CD-X    4    4.00        180.0     2.         Junmei et al, 1999
+-X -CD-CT-X    6    0.00          0.0     2.         Junmei et al, 1999
+-X -CD-CM-X    4   26.60        180.0     2.         Junmei et al, 1999
+-X -CK-N*-X    4    6.80        180.0     2.         JCC,7,(1986),230
+-X -CK-NB-X    2   20.00        180.0     2.         JCC,7,(1986),230
+-X -CM-CM-X    4   26.60        180.0     2.         intrpol.bsd.on C6H6
+-X -CM-CT-X    6    0.00          0.0     3.         JCC,7,(1986),230
+-X -CM-N*-X    4    7.40        180.0     2.         JCC,7,(1986),230
+-X -CM-OS-X    2    2.10        180.0     2.         Junmei et al, 1999
+-X -CN-NA-X    4    6.10        180.0     2.         reinterpolated 93'
+-X -CQ-NC-X    2   13.60        180.0     2.         JCC,7,(1986),230
+-X -CT-CT-X    9    1.40          0.0     3.         JCC,7,(1986),230
+-X -CT-CY-X    3    0.00          0.0     1.         Junmei et al, 1999
+-X -CT-CZ-X    3    0.00          0.0     1.         Junmei et al, 1999
+-X -CT-N -X    6    0.00          0.0     2.         JCC,7,(1986),230
+-X -CT-N*-X    6    0.00          0.0     2.         JCC,7,(1986),230
+-X -CT-N2-X    6    0.00          0.0     3.         JCC,7,(1986),230
+-X -CT-NT-X    6    1.80          0.0     3.         Junmei et al, 1999
+-X -CT-N3-X    9    1.40          0.0     3.         JCC,7,(1986),230
+-X -CT-OH-X    3    0.50          0.0     3.         JCC,7,(1986),230
+-X -CT-OS-X    3    1.15          0.0     3.         JCC,7,(1986),230
+-X -CT-S -X    3    1.00          0.0     3.         JCC,7,(1986),230
+-X -CT-SH-X    3    0.75          0.0     3.         JCC,7,(1986),230
+-X -C*-CB-X    4    6.70        180.0     2.         intrpol.bsd.onC6H6aa
+-X -C*-CT-X    6    0.00          0.0     2.         JCC,7,(1986),230
+-X -C*-CW-X    4   26.10        180.0     2.         intrpol.bsd.on C6H6
+-X -CR-NA-X    4    9.30        180.0     2.         JCC,7,(1986),230
+-X -CR-NB-X    2   10.00        180.0     2.         JCC,7,(1986),230
+-X -CV-NB-X    2    4.80        180.0     2.         JCC,7,(1986),230
+-X -CW-NA-X    4    6.00        180.0     2.         JCC,7,(1986),230
+-X -OH-P -X    3    0.75          0.0     3.         JCC,7,(1986),230
+-X -OS-P -X    3    0.75          0.0     3.         JCC,7,(1986),230
+-N -CT-C -N    1    1.700       180.000  -1.
+-N -CT-C -N    1    2.000       180.000   2.
+-C -N -CT-C    1    0.850       180.000  -2.
+-C -N -CT-C    1    0.800         0.000   1.
+-CT-CT-N -C    1    0.50        180.0    -4.         phi,psi,parm94
+-CT-CT-N -C    1    0.15        180.0    -3.         phi,psi,parm94
+-CT-CT-N -C    1    0.00          0.0    -2.         JCC,7,(1986),230
+-CT-CT-N -C    1    0.53          0.0     1.         phi,psi,parm94
+-CT-CT-C -N    1    0.100         0.0    -4.         phi,psi,parm94
+-CT-CT-C -N    1    0.07          0.0     2.         phi,psi,parm94
+-H -N -C -O    1    2.50        180.0    -2.         JCC,7,(1986),230
+-H -N -C -O    1    2.00          0.0     1.         J.C.cistrans-NMA DE
+-CT-S -S -CT   1    3.50          0.0    -2.         JCC,7,(1986),230
+-CT-S -S -CT   1    0.60          0.0     3.         JCC,7,(1986),230
+-OH-P -OS-CT   1    0.25          0.0    -3.         JCC,7,(1986),230
+-OH-P -OS-CT   1    1.20          0.0     2.         gg&gt ene.631g*/mp2
+-OS-P -OS-CT   1    0.25          0.0    -3.         JCC,7,(1986),230
+-OS-P -OS-CT   1    1.20          0.0     2.         gg&gt ene.631g*/mp2
+-H1-CT-C -O    1    0.80          0.0    -1.         Junmei et al, 1999
+-H1-CT-C -O    1    0.00          0.0    -2.         Explicit of wild card X-C-CT-X
+-H1-CT-C -O    1    0.08        180.0     3.         Junmei et al, 1999
+-HC-CT-C -O    1    0.80          0.0    -1.         Junmei et al, 1999
+-HC-CT-C -O    1    0.00          0.0    -2.         Explicit of wild card X-C-CT-X
+-HC-CT-C -O    1    0.08        180.0     3.         Junmei et al, 1999
+-HC-CT-CT-HC   1    0.15          0.0     3.         Junmei et al, 1999
+-HC-CT-CT-CT   1    0.16          0.0     3.         Junmei et al, 1999
+-HC-CT-CM-CM   1    0.38        180.0    -3.         Junmei et al, 1999
+-HC-CT-CM-CM   1    1.15          0.0     1.         Junmei et al, 1999
+-HO-OH-CT-CT   1    0.16          0.0    -3.         Junmei et al, 1999
+-HO-OH-CT-CT   1    0.25          0.0     1.         Junmei et al, 1999
+-HO-OH-C -O    1    2.30        180.0    -2.         Junmei et al, 1999
+-HO-OH-C -O    1    0.00          0.0     1.         Junmei et al, 2011, actyle acid density optimization
+-CM-CM-C -O    1    2.175       180.0    -2.         Junmei et al, 1999
+-CM-CM-C -O    1    0.30          0.0     3.         Junmei et al, 1999
+-CT-CM-CM-CT   1    6.65        180.0    -2.         Junmei et al, 1999
+-CT-CM-CM-CT   1    1.90        180.0     1.         Junmei et al, 1999
+-CT-CT-CT-CT   1    0.18          0.0    -3.         Junmei et al, 1999
+-CT-CT-CT-CT   1    0.25        180.0    -2.         Junmei et al, 1999
+-CT-CT-CT-CT   1    0.20        180.0     1.         Junmei et al, 1999
+-CT-CT-NT-CT   1    0.30          0.0    -3.         Junmei et al, 1999
+-CT-CT-NT-CT   1    0.48        180.0     2.         Junmei et al, 1999
+-CT-CT-OS-CT   1    0.383         0.0    -3.
+-CT-CT-OS-CT   1    0.1         180.0     2.
+-CT-CT-OS-C    1    0.383         0.0    -3.         Junmei et al, 1999
+-CT-CT-OS-C    1    0.80        180.0     1.         Junmei et al, 1999
+-CT-OS-CT-OS   1    0.10          0.0    -3.         Junmei et al, 1999
+-CT-OS-CT-OS   1    0.85        180.0    -2.         Junmei et al, 1999
+-CT-OS-CT-OS   1    1.35        180.0     1.         Junmei et al, 1999
+-CT-OS-CT-N*   1    0.383         0.0    -3.         parm98.dat, TC,PC,PAK
+-CT-OS-CT-N*   1    0.65          0.0     2.         Piotr et al.
+-CT-CZ-CZ-HZ   1    0.00          0.0     1.         Junmei et al, 1999
+-O -C -OS-CT   1    2.70        180.0    -2.         Junmei et al, 1999
+-O -C -OS-CT   1    1.40        180.0     1.         Junmei et al, 1999
+-OS-CT-N*-CK   1    0.00        000.0    -2.         parm98, TC,PC,PAK
+-OS-CT-N*-CK   1    2.50          0.0     1.         parm98, TC,PC,PAK
+-OS-CT-N*-CM   1    0.00        000.0    -2.         parm98, TC,PC,PAK
+-OS-CT-N*-CM   1    2.50          0.0     1.         parm98, TC,PC,PAK
+-OS-CT-CT-OS   1    0.144         0.0    -3.         parm98, TC,PC,PAK
+-OS-CT-CT-OS   1    1.175         0.0     2.         Piotr et al.     
+-OS-CT-CT-OH   1    0.144         0.0    -3.         parm98, TC,PC,PAK
+-OS-CT-CT-OH   1    1.175         0.0     2.         parm98, TC,PC,PAK
+-OH-CT-CT-OH   1    0.144         0.0    -3.         parm98, TC,PC,PAK
+-OH-CT-CT-OH   1    1.175         0.0     2.         parm98, TC,PC,PAK 
+-F -CT-CT-F    1    0.000         0.0    -3.         JCC,7,(1986),230
+-F -CT-CT-F    1    1.20        180.0     1.         Junmei et al, 1999
+-Cl-CT-CT-Cl   1    0.000         0.0    -3.         JCC,7,(1986),230
+-Cl-CT-CT-Cl   1    0.45        180.0     1.         Junmei et al, 1999
+-Br-CT-CT-Br   1    0.000         0.0    -3.         JCC,7,(1986),230
+-Br-CT-CT-Br   1    0.00        180.0     1.         Junmei et al, 1999
+-H1-CT-CT-OS   1    0.000         0.0    -3.         JCC,7,(1986),230
+-H1-CT-CT-OS   1    0.25          0.0     1.         Junmei et al, 1999
+-H1-CT-CT-OH   1    0.000         0.0    -3.         JCC,7,(1986),230
+-H1-CT-CT-OH   1    0.25          0.0     1.         Junmei et al, 1999
+-H1-CT-CT-F    1    0.000         0.0    -3.         JCC,7,(1986),230
+-H1-CT-CT-F    1    0.19          0.0     1.         Junmei et al, 1999
+-H1-CT-CT-Cl   1    0.000         0.0    -3.         JCC,7,(1986),230
+-H1-CT-CT-Cl   1    0.25          0.0     1.         Junmei et al, 1999
+-H1-CT-CT-Br   1    0.000         0.0    -3.         JCC,7,(1986),230
+-H1-CT-CT-Br   1    0.55          0.0     1.         Junmei et al, 1999
+-HC-CT-CT-OS   1    0.000         0.0    -3.         JCC,7,(1986),230
+-HC-CT-CT-OS   1    0.25          0.0     1.         Junmei et al, 1999
+-HC-CT-CT-OH   1    0.000         0.0    -3.         JCC,7,(1986),230
+-HC-CT-CT-OH   1    0.25          0.0     1.         Junmei et al, 1999
+-HC-CT-CT-F    1    0.000         0.0    -3.         JCC,7,(1986),230
+-HC-CT-CT-F    1    0.19          0.0     1.         Junmei et al, 1999
+-HC-CT-CT-Cl   1    0.000         0.0    -3.         JCC,7,(1986),230
+-HC-CT-CT-Cl   1    0.25          0.0     1.         Junmei et al, 1999
+-HC-CT-CT-Br   1    0.000         0.0    -3.         JCC,7,(1986),230
+-HC-CT-CT-Br   1    0.55          0.0     1.         Junmei et al, 1999
+-H1-CT-NT-LP   1    0.000         0.000   3.
+-CT-CT-NT-LP   1    0.000         0.000   3.
+-CT-C -N -LP   1    0.000       180.000   2.
+-O -C -N -LP   1    0.000       180.000   2.
+-H1-CT-OH-LP   1    0.000         0.000   3.
+-CT-CT-OH-LP   1    0.000         0.000   3.
+-H1-CT-OS-LP   1    0.000         0.000   3.
+-H2-CT-OS-LP   1    0.000         0.000   3.
+-CT-CT-OS-LP   1    0.000         0.000   3.
+-CM-CM-OS-LP   1    0.000       180.000   2.
+-HA-CM-OS-LP   1    0.000       180.000   2.
+-H4-CM-OS-LP   1    0.000       180.000   2.
+-
+-X -X -C -O          10.5         180.          2.           JCC,7,(1986),230
+-X -O2-C -O2         10.5         180.          2.           JCC,7,(1986),230
+-X -X -N -H          1.0          180.          2.           JCC,7,(1986),230
+-X -X -N2-H          1.0          180.          2.           JCC,7,(1986),230
+-X -X -NA-H          1.0          180.          2.           JCC,7,(1986),230
+-X -N2-CA-N2         10.5         180.          2.           JCC,7,(1986),230
+-X -CT-N -CT         1.0          180.          2.           JCC,7,(1986),230
+-X -X -CA-HA         1.1          180.          2.           bsd.on C6H6 nmodes
+-X -X -CW-H4         1.1          180.          2.
+-X -X -CR-H5         1.1          180.          2.
+-X -X -CV-H4         1.1          180.          2.
+-X -X -CQ-H5         1.1          180.          2.
+-X -X -CK-H5         1.1          180.          2.
+-X -X -CM-H4         1.1          180.          2.
+-X -X -CM-HA         1.1          180.          2.
+-X -X -CA-H4         1.1          180.          2.           bsd.on C6H6 nmodes 
+-X -X -CA-H5         1.1          180.          2.           bsd.on C6H6 nmodes
+-CB-CK-N*-CT         1.0          180.          2.
+-C -CM-N*-CT         1.0          180.          2.           dac guess, 9/94
+-C -CM-CM-CT         1.1          180.          2. 
+-CT-O -C -OH         10.5         180.          2.
+-CT-CV-CC-NA         1.1          180.          2.
+-CT-CW-CC-NB         1.1          180.          2.
+-CT-CW-CC-NA         1.1          180.          2.
+-CB-CT-C*-CW         1.1          180.          2.
+-CA-CA-CA-CT         1.1          180.          2. 
+-C -CM-CM-CT         1.1          180.          2.           dac guess, 9/94
+-CM-N2-CA-NC         1.1          180.          2.           dac guess, 9/94
+-CB-N2-CA-NC         1.1          180.          2.           dac, 10/94
+-N2-NA-CA-NC         1.1          180.          2.           dac, 10/94
+-CA-CA-C -OH         1.1          180.          2.           (not used in tyr!)
+-CA-CA-CA-OH         1.1          180.          2.           in tyr
+-H5-O -C -OH         1.1          180.          2.           Junmei et al.1999
+-H5-O -C -OS         1.1          180.          2.           
+-CM-CT-CM-HA         1.1          180.          2.           Junmei et al.1999
+-Br-CA-CA-CA         1.1          180.          2.           Junmei et al.1999
+-CM-H4-C -O          1.1          180.          2.           Junmei et al.1999
+-C -CT-N -H          1.1          180.          2.           Junmei et al.1999
+-C -CT-N -O          1.1          180.          2.           Junmei et al.1999
+-
+-  HW  OW  0000.     0000.                                4.  flag for fast water
+-
+-N   NA  N2  N*  NC  NB  NY
+-C*  CA  CB  CC  CD  CK  CM  CN  CQ  CR  CV  CW  CZ
+-
+-MOD4      RE
+-  H           0.9000  0.0008             Junmei optimization
+-  HO          0.6000  0.0000             Junmei optimization
+-  HS          0.6000  0.0157             Junmei optimization
+-  HC          1.3992  0.0326             Junmei optimization
+-  H0          1.2992  0.0326             Junmei optimization
+-  H1          1.2992  0.0326             Junmei optimization
+-  H2          1.1992  0.0326             Junmei optimization
+-  H3          1.0992  0.0326             Junmei optimization
+-  H4          1.5424  0.0052             Junmei optimization
+-  H5          1.4924  0.0052             Junmei optimization
+-  HA          1.5924  0.0052             Junmei optimization
+-  HP          0.9000  0.0008             Junmei optimization
+-  HZ          1.4590  0.0150             H bonded to sp C (Howard et al JCC 16)
+-  HW          0.0000  0.0000             TIP3P, POL3, SPC/E water models
+-  OW          1.7980  0.1560             POL3 water model
+-  O           1.6582  0.2146             Junmei optimization
+-  OH          1.7895  0.0752             Junmei optimization
+-  O2          1.4062  1.3962             Junmei optimization
+-  OS          1.7127  0.1385             Junmei optimization
+-  C           2.1034  0.0267             Junmei optimization
+-  C2          1.8446  0.1290             Junmei optimization
+-  CY          1.9295  0.1836             Junmei optimization
+-  CT          2.0242  0.0538             Junmei optimization
+-  C*          1.8738  0.1068             Junmei optimization
+-  N           1.8714  0.1312             Junmei optimization
+-  NT          1.9500  0.0450             Junmei optimization
+-  N3          1.9500  0.0450             Junmei optimization
+-  S           1.9980  0.2530             Junmei optimization
+-  SH          1.9980  0.2530             Junmei optimization
+-  P           2.1000  0.2000             JCC,7,(1986),230; 
+-  IM          2.47    0.1                Cl- Smith & Dang, JCP 1994,100:5,3757
+-  Li          1.1370  0.0183             Li+ Aqvist JPC 1990,94,8021. (adapted)
+-  IP          1.8680  0.00277            Na+ Aqvist JPC 1990,94,8021. (adapted)
+-  Na          1.8680  0.00277            Na+ Aqvist JPC 1990,94,8021. (adapted)
+-  K           2.6580  0.000328           K+  Aqvist JPC 1990,94,8021. (adapted)
+-  Rb          2.9560  0.00017            Rb+ Aqvist JPC 1990,94,8021. (adapted)
+-  Cs          3.3950  0.0000806          Cs+ Aqvist JPC 1990,94,8021. (adapted)
+-  MG          0.7926  0.8947             Mg2+ Aqvist JPC 1990,94,8021.(adapted)
+-  C0          1.7131  0.459789           Ca2+ Aqvist JPC 1990,94,8021.(adapted)
+-  Zn          1.10    0.0125             Zn2+, Merz,PAK, JACS,113,8262,(1991) 
+-  F           1.75    0.061              Gough et al. JCC 13,(1992),963.
+-  Cl          1.948   0.265              Fox, JPCB,102,8070,(98),flex.mdl CHCl3
+-  Br          2.22    0.320              Junmei(?)
+-  I           2.35    0.40               JCC,7,(1986),230;  
+-  IB          5.0     0.1                solvated ion for vacuum approximation
+-  LP          0.00    0.0000             lone pair
+- 
+-END
+-
+-
+-####################################################
+-Polarizabilities:
+-Mg2+  0.120
+-F-    0.9743
+-
+-
+-additional parameters of LP
+-
+-H1-CT-NT-LP   1       0.000       0.000       3.000
+-CT-CT-NT-LP   1       0.000       0.000       3.000
+-CT-C -N -LP   1       0.000     180.000       2.000
+-O -C -N -LP   1       0.000     180.000       2.000
+-H1-CT-OH-LP   1       0.000       0.000       3.000
+-CT-CT-OH-LP   1       0.000       0.000       3.000
+-H1-CT-OS-LP   1       0.000       0.000       3.000
+-H2-CT-OS-LP   1       0.000       0.000       3.000
+-CT-CT-OS-LP   1       0.000       0.000       3.000
+-CM-CM-OS-LP   1       0.000     180.000       2.000
+-HA-CM-OS-LP   1       0.000     180.000       2.000
+-H4-CM-OS-LP   1       0.000     180.000       2.000
+-
+-
+diff --git a/patch_amber.py b/patch_amber.py
+index 84d90c4..2b5ae7a 100755
+--- a/patch_amber.py
++++ b/patch_amber.py
+@@ -25,7 +25,7 @@ Acknowledgements/Contributions from others
+    * Tyler Luchko made helpful contributions to the user-interface
+ """
+ # Load common os module and package into top level namespace
+-from os import path, getenv
++from os import path, getenv, chmod
+ 
+ # Global variables. Other ones that change less frequently can be found below
+ # the Patch class definitions.
+@@ -230,9 +230,11 @@ class Patch(object):
+       """
+       # This regex matches lines that start like "+++ path/to/file.cpp"
+       modfile = re.compile(r'\+\+\+ \.*\/*[\w\-\/\.\+]+[\w\-\.\+]+\.*\w*')
+-      selffile = re.compile('\\+\\+\\+ %s' % path.split(sys.argv[0])[1])
++      selffile = re.compile(r'\+\+\+ %s' % path.split(sys.argv[0])[1])
++      newfile = re.compile(r'new file mode (\d{3})+')
+       patch = open(self.name, 'r')
+       files_modified = []
++      newfile_modes = []
+       for line in patch:
+          if modfile.match(line):
+             filename = modfile.findall(line)[0].strip('+++').strip()
+@@ -247,8 +249,17 @@ class Patch(object):
+          elif selffile.match(line):
+             filename = path.split(sys.argv[0])[1]
+             if not filename in files_modified: files_modified.append(filename)
++         elif newfile.match(line):
++            ftmp = newfile.match(line).groups()
++            if isinstance(ftmp, tuple):
++               if len(ftmp) == 2:
++                  newfile_modes.append(ftmp[1])
++               elif len(ftmp) == 1:
++                  newfile_modes.append(ftmp[0])
++            elif isinstance(ftmp, str):
++               newfile_modes.append(ftmp)
+       patch.close()
+-      return files_modified
++      return files_modified, newfile_modes
+ 
+    #========================================
+ 
+@@ -331,7 +342,7 @@ class PatchBz2(Patch):
+       
+       print 'Decompressing %s with %s' % (patch_file, bunzip)
+ 
+-      process = Popen([bunzip, patch_file], stdout=PIPE, stderr=PIPE)
++      process = Popen([bunzip, '-f', patch_file], stdout=PIPE, stderr=PIPE)
+ 
+       (output, error) = process.communicate('')
+ 
+@@ -340,8 +351,8 @@ class PatchBz2(Patch):
+                           patch_file, error))
+          sys.exit(1)
+ 
+-      # Get rid of the file extension
+-      patch_file = patch_file.strip('.bz2')
++      # Get rid of the file extension (.bz2)
++      patch_file = patch_file[:len(patch_file)-4]
+       Patch.__init__(self, patch_file)
+ 
+ #~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~
+@@ -370,7 +381,7 @@ class PatchGz(Patch):
+       
+       print 'Decompressing %s with %s' % (patch_file, gunzip)
+ 
+-      process = Popen([gunzip, patch_file], stdout=PIPE, stderr=PIPE)
++      process = Popen([gunzip, '-f', patch_file], stdout=PIPE, stderr=PIPE)
+ 
+       (output, error) = process.communicate('')
+ 
+@@ -379,14 +390,14 @@ class PatchGz(Patch):
+                           patch_file, error))
+          sys.exit(1)
+ 
+-      # Get rid of the file extension
+-      patch_file = patch_file.strip('.gz')
++      # Get rid of the file extension (.gz)
++      patch_file = patch_file[:len(patch_file)-3]
+       Patch.__init__(self, patch_file)
+ 
+ #~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~+~
+ 
+ # The list of searched suffixes for patch names (ASCII, Bzip2, Gzip)
+-patch_suffixes = ('', '.bz2', '.gz')
++patch_suffixes = ('', '.bz2_', '.gz_')
+ # The corresponding classes for each patch suffix listed above IN SAME ORDER
+ patch_classes = (Patch, PatchBz2, PatchGz)
+ # This is the description printed with the program usage message
+@@ -413,14 +424,18 @@ def download_patch(search_location, patch_number, save_loc):
+          if 'timed out' in str(err):
+             print >> sys.stderr, 'Timed out connecting to server'
+             sys.exit(1)
+-         raise err
++         continue
+       # A 404 code means we didn't find it
+       if url_patch.getcode() == 404:
+          url_patch.close()
+          continue
+       # Otherwise we found it, so use urlretrieve to download the file
+       url_patch.close()
+-      local_patch = path.join(save_loc, fixname)
++      # Hack for compressed patch files
++      if fixname.endswith('_'):
++         local_patch = path.join(save_loc, fixname[:len(fixname)-1])
++      else:
++         local_patch = path.join(save_loc, fixname)
+       print '  Downloading %s' % fixname
+       urllib.urlretrieve(search_location + fixname, local_patch)
+       # Now that we have the patch file saved, return the appropriate PatchClass
+@@ -484,8 +499,8 @@ def describe_patch(patch, full=True, hide_prefix=True):
+    if patch.author(): print '  Author:         ', patch.author()
+    if patch.date(): print '  Created on:     ', patch.date()
+    if patch.programs(): print '  Programs fixed: ', ', '.join(patch.programs())
+-   if patch.files_edited():
+-      print '  Files affected: ', ('\n%19s' % ' ').join(patch.files_edited())
++   if patch.files_edited()[0]:
++      print '  Files affected: ', ('\n%19s' % ' ').join(patch.files_edited()[0])
+    if full: print '\n', patch.description()
+    print ''
+ 
+@@ -513,18 +528,32 @@ def _files_present(patch):
+    return -2: Same as -1, except we also modify this program (as in 2)
+    """
+ 
+-   edfiles = patch.files_edited()
++   edfiles, newmodes = patch.files_edited()
+    if not edfiles:
+       print >> sys.stderr, ('Fatal Error: The patch "%s" does not edit any ' +
+                             'files!') % patch.name
+       sys.exit(1)
+    fname = edfiles[0]
+    ret_code = 1
++   newfile_count = 0
+    if ('src/sander' in fname or 'src/pmemd' in fname) and not path.isdir(
+             path.join(getenv('AMBERHOME'), 'src', 'pmemd', 'src')):
+       ret_code = 0
+    if fname == path.split(sys.argv[0])[1]:
+       ret_code = 2
++   elif not path.exists(path.join(getenv('AMBERHOME'), fname)):
++      _mkdir(path.join(getenv('AMBERHOME'), path.split(fname)[0]))
++      print 'Creating file %s' % (path.join(getenv('AMBERHOME'), fname))
++      tmpfile = open(path.join(getenv('AMBERHOME'), fname), 'w')
++      tmpfile.close()
++      try:
++         print 'Changing mode to %s' % (newmodes[0])
++         # chmod takes octal numbers, so convert the octal number
++         chmod(path.join(getenv('AMBERHOME'), fname), int(newmodes[0], 8))
++         newfile_count += 1
++      except IndexError:
++         # If our patch didn't have mode info, don't pitch a fit
++         pass
+    for i in range(1,len(edfiles)):
+       fname = edfiles[i]
+       # If ret_code is already 1, then our first file matched one we had,
+@@ -544,6 +573,15 @@ def _files_present(patch):
+          print 'Creating file %s' % (path.join(getenv('AMBERHOME'), fname))
+          tmpfile = open(path.join(getenv('AMBERHOME'), fname), 'w')
+          tmpfile.close()
++         try:
++            print 'Changing mode to %s' % (newmodes[newfile_count])
++            # chmod takes octal numbers, so convert the octal number
++            chmod(path.join(getenv('AMBERHOME'), fname),
++                  int(newmodes[newfile_count], 8))
++            newfile_count += 1
++         except IndexError:
++            # Don't pitch a fit if our patch file didn't have permission info
++            pass
+ 
+    return ret_code
+ 
+@@ -775,7 +813,7 @@ if __name__ == '__main__':
+          sys.exit(1)
+       if opt.apply_patch: single_patch = Patch(opt.apply_patch)
+       else: single_patch = Patch(opt.reverse_patch)
+-      if not single_patch.files_edited():
++      if not single_patch.files_edited()[0]:
+          print >> sys.stderr, 'Fatal Error: Bad patch. Could not find the ' + \
+                'files that were supposed to be edited!'
+       # Print out message based on whether we're applying forward or reverse
diff --git a/sci-chemistry/ambertools/files/ambertools-12-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-12-gentoo.patch
new file mode 100644
index 000000000..b0e7cf40d
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-12-gentoo.patch
@@ -0,0 +1,1251 @@
+diff --git a/AmberTools/src/Makefile b/AmberTools/src/Makefile
+index e5c0ded..ce8f883 100644
+--- a/AmberTools/src/Makefile
++++ b/AmberTools/src/Makefile
+@@ -13,12 +13,6 @@ install: $(INSTALLTYPE)
+ serial: configured_serial THIRDPARTY $(MTKPP)
+ 	@echo "Starting installation of ${AMBERTOOLS} serial at `date`".
+ #	utility routines and libraries:
+-	(cd ucpp-1.3 && $(MAKE) $(UCPP) )
+-	(cd byacc && $(MAKE) install )
+-	(cd arpack && $(MAKE) install );
+-	(cd lapack && $(MAKE) $(LAPACK) )
+-	(cd blas && $(MAKE) $(BLAS) )
+-	(cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
+ 	(cd etc && $(MAKE) install )
+ 	(cd chamber && $(MAKE) install )
+ 	(cd pbsa && $(MAKE) install )
+@@ -34,13 +28,11 @@ serial: configured_serial THIRDPARTY $(MTKPP)
+ 	(cd cpptraj && $(MAKE) install)
+ 
+ #   miscellaneous:
+-	(cd reduce && $(MAKE) install )
+ 
+ #   leap
+ 	(cd leap && $(MAKE) install )
+ 
+ #   nab:
+-	(cd cifparse && $(MAKE) install )
+ 	(cd sff && $(MAKE) install )
+ 	(cd pbsa && $(MAKE) libinstall )
+ 	(cd rism && $(MAKE) $(RISM) )
+@@ -77,17 +69,10 @@ serial: configured_serial THIRDPARTY $(MTKPP)
+ 	@echo "Installation of ${AMBERTOOLS} serial is complete at `date`."
+ 	@echo ""
+ 
+-nabonly: $(NETCDF) $(XBLAS)  
++nabonly: $(XBLAS)
+ #	utility routines and libraries:
+-	(cd ucpp-1.3 && $(MAKE) $(UCPP) )
+-	(cd byacc && $(MAKE) install )
+-	(cd arpack && $(MAKE) install );
+-	(cd lapack && $(MAKE) $(LAPACK) )
+-	(cd blas && $(MAKE) $(BLAS) )
+-	(cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
+ 	(cd pbsa && $(MAKE) libinstall )
+ 	(cd rism && $(MAKE) $(RISM) )
+-	(cd cifparse && $(MAKE) install )
+ 	(cd sff && $(MAKE) install )
+ 	(cd nab && $(MAKE) install )
+ 	(cd nss && $(MAKE) install )
+@@ -119,8 +104,6 @@ parallel: configured_parallel THIRDPARTY
+ 	(cd sff && $(MAKE) libsff_mpi )
+ #	(cd pbsa && $(MAKE) clean && $(MAKE) install.parallel )
+ 	(cd pbsa && $(MAKE) libinstall )
+-	(cd byacc && $(MAKE) install )
+-	(cd ucpp-1.3 && $(MAKE) $(UCPP) )
+ #	(cd mdgx && $(MAKE) parallel )
+ 	(if [ "$(RISM)" = "yes" ]; then \
+ 		cd rism && $(MAKE) install_mpi ; \
+@@ -162,18 +145,11 @@ configured_parallel: configured
+ 	)
+ 
+ clean::  netcdf_clean
+-	-(cd ucpp-1.3 && $(MAKE) clean )
+-	-(cd byacc && $(MAKE) clean )
+-	-(cd cifparse && $(MAKE) clean )
+ 	-(cd nab && $(MAKE) clean )
+ 	-(cd sff && $(MAKE) clean )
+ 	-(cd nss && $(MAKE) clean )
+ 	-(cd leap && $(MAKE) clean )
+-	-(cd arpack && $(MAKE) clean )
+-	-(cd blas && $(MAKE) clean )
+ 	-(cd xblas && $(MAKE) clean )
+-	-(cd lapack && $(MAKE) clean )
+-	-(cd c9x-complex && $(MAKE) clean )
+ 	-(cd etc && $(MAKE) clean )
+ 	-(cd chamber && $(MAKE) clean )
+ 	-(cd pbsa && $(MAKE) clean )
+@@ -182,15 +158,12 @@ clean::  netcdf_clean
+ 	-(cd lib && $(MAKE) clean )
+ 	-(cd ptraj && $(MAKE) clean )
+ 	-(cd cpptraj && $(MAKE) clean)
+-	-(cd reduce && $(MAKE) clean )
+ 	-(cd mtkpp && $(MAKE) clean )
+ 	-(cd mdgx && $(MAKE) clean )
+ 	-(cd xtalutil/CPrograms && $(MAKE) clean )
+ 	-(cd xray && $(MAKE) clean )
+ 	-(cd paramfit && $(MAKE) clean )
+ 	-(cd rism && $(MAKE) clean )
+-	-(cd fftw-3.3 && $(MAKE) clean )
+-	-($(RM) -f fftw-3.3/mpi/fftw3-mpi.f03 )
+ 	-(cd mmpbsa_py && $(MAKE) clean )
+ 	-(cd parmed && $(MAKE) clean )
+ 
+@@ -201,18 +174,11 @@ netcdf_clean:
+ 	-(cd netcdf/bin && rm -f *)
+ 
+ uninstall:
+-	-(cd ucpp-1.3 && $(MAKE) uninstall )
+-	-(cd byacc && $(MAKE) uninstall )
+-	-(cd cifparse && $(MAKE) uninstall )
+ 	-(cd nab && $(MAKE) uninstall )
+ 	-(cd sff && $(MAKE) uninstall )
+ 	-(cd nss && $(MAKE) uninstall )
+ 	-(cd leap && $(MAKE) uninstall )
+-	-(cd arpack && $(MAKE) uninstall )
+-	-(cd blas && $(MAKE) uninstall )
+ 	-($(RM) -f $(LIBDIR)/libxblas.a )
+-	-(cd lapack && $(MAKE) uninstall )
+-	-(cd c9x-complex && $(MAKE) uninstall )
+ 	-(cd etc && $(MAKE) uninstall )
+ 	-(cd chamber && $(MAKE) uninstall )
+ 	-(cd pbsa && $(MAKE) uninstall )
+@@ -220,7 +186,6 @@ uninstall:
+ 	-(cd sqm && $(MAKE) uninstall )
+ 	-(cd lib && $(MAKE) uninstall )
+ 	-(cd ptraj && $(MAKE) uninstall )
+-	-(cd reduce && $(MAKE) uninstall )
+ 	-(cd mdgx && $(MAKE) uninstall )
+ 	-(cd xtalutil/CPrograms && $(MAKE) uninstall )
+ 	-(cd xray && $(MAKE) uninstall )
+@@ -228,15 +193,12 @@ uninstall:
+ 	-(cd paramfit && $(MAKE) uninstall )
+ 	-(cd rism && $(MAKE) uninstall )
+ 	-(cd netcdf/src && $(MAKE) uninstall)
+-	-(cd fftw-3.3 && $(MAKE) uninstall)
+ 	-(cd cpptraj && $(MAKE) uninstall)
+ 	-(cd mmpbsa_py && $(MAKE) uninstall )
+ 	-(cd parmed && $(MAKE) uninstall )
+ 	-(cd amberlite && $(MAKE) uninstall )
+ 	-/bin/rm -f ../test/numprocs
+ 	-/bin/rm -fr $(BINDIR)/ncmpidump $(BINDIR)/ncmpigen $(BINDIR)/ncvalid $(LIBDIR)/libnetcdf.a $(INCDIR)/mtkpp
+-	-(cd $(LIBDIR) && /bin/rm -f libxblas-amb.a libfftw3_mpi.a libfftw3_mpi.la)
+-	-(cd $(INCDIR) && /bin/rm -f fftw3-mpi.f03 fftw3-mpi.h)
+ 
+ $(INCDIR)/netcdf.mod:
+ 	cd netcdf/src && $(MAKE) && $(MAKE) -j 1 install
+@@ -247,7 +209,7 @@ $(LIBDIR)/libxblas-amb.a:
+ $(LIBDIR)/libfftw3.a $(LIBDIR)/libfftw3_mpi.a: 
+ 	cd fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install;
+ 
+-THIRDPARTY: $(NETCDF) $(XBLAS) $(FFTW3)
++THIRDPARTY: $(XBLAS)
+ 
+ cuda:
+ 	@echo "$(AMBERTOOLS) has no CUDA-enabled components"
+diff --git a/AmberTools/src/configure2 b/AmberTools/src/configure2
+index 25d3f0a..1ad86e6 100755
+--- a/AmberTools/src/configure2
++++ b/AmberTools/src/configure2
+@@ -387,11 +387,11 @@ omp_flag=
+ mpi_flag=
+ lex=flex
+ flibs_mkl=
+-lapack=install
+-blas=install
++lapack=skip
++blas=skip
+ f2c=skip
+-ucpp=install
+-cpp="ucpp -l"
++ucpp=skip
++cpp="\$(EPREFIX)/usr/bin/ucpp -l"
+ 
+ #-----------------------------------
+ # skip building of xleap?
+@@ -618,13 +618,14 @@ gnu)
+     flibs_arch="-lgfortran -w"
+     flibsf_arch=
+     cc=gcc
+-    cflags=
++    cflags="GENTOO_CFLAGS"
+     ambercflags=""
+     cplusplus=g++
+-    cxxflags=
++    cxxflags="GENTOO_CXXFLAGS"
+     ambercxxflags=""
+     fc=gfortran
+-    fflags=
++    fflags="GENTOO_FFLAGS"
++    ldflags="GENTOO_LDFLAGS"
+     staticflag='-static'
+     
+     # If -noopt has been requested, force lack of optimisation;
+@@ -645,11 +646,11 @@ gnu)
+       foptflags=""
+     else
+       cnooptflags=
+-      coptflags="-O3"
++      coptflags="GENTOO_CFLAGS"
+       cxxnooptflags=
+-      cxxoptflags="-O3"
++      cxxoptflags="GENTOO_CXXFLAGS"
+       fnooptflags="-O0"
+-      foptflags="-O3"
++      foptflags="GENTOO_FFLAGS"
+     fi
+     
+     # Debugging options
+@@ -2026,26 +2027,26 @@ EOF
+       if [ "$sse" = "yes" ]; then
+           enable_sse="--enable-sse2=yes" # --enable-avx=yes"
+       fi
+-      cd fftw-3.3 && \
+-	  ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
+-          --enable-static=yes \
+-          $enable_mpi $enable_debug $enable_sse\
+-	  CC="$cc" CFLAGS="$cflags $coptflags" \
+-          F77="$fc" FFLAGS="$fflags $foptflags" \
+-          FLIBS="$flibs_arch" \
+-	  > ../fftw3_config.log 2>&1
+-      ncerror=$?
+-      if [ $ncerror -gt 0 ]; then
+-          echo "    Error: FFTW configure returned $ncerror"
+-          echo "    FFTW configure failed! Check the fftw3_config.log file"
+-          echo "    in the $AMBERHOME/AmberTools/src diretory."
+-          exit 1
+-      else
+-          echo "    fftw-3.3 configure succeeded."
+-      fi
+-      cd ..
++#      cd fftw-3.3 && \
++#	  ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
++#          --enable-static=yes \
++#          $enable_mpi $enable_debug $enable_sse\
++#	  CC="$cc" CFLAGS="$cflags $coptflags" \
++#          F77="$fc" FFLAGS="$fflags $foptflags" \
++#          FLIBS="$flibs_arch" \
++#	  > ../fftw3_config.log 2>&1
++#      ncerror=$?
++#      if [ $ncerror -gt 0 ]; then
++#          echo "    Error: FFTW configure returned $ncerror"
++#          echo "    FFTW configure failed! Check the fftw3_config.log file"
++#          echo "    in the $AMBERHOME/AmberTools/src diretory."
++#          exit 1
++#      else
++#          echo "    fftw-3.3 configure succeeded."
++#      fi
++#      cd ..
+       fftw3="FFTW3"
+-      flibs_fftw3="-lfftw3"
++      flibs_fftw3="GENTOO_FFTW3_LIBS"
+       fftw3="\$(LIBDIR)/libfftw3.a"
+       if [ "$mpi" = 'yes' ]; then
+           flibs_fftw3="-lfftw3_mpi $flibs_fftw3"
+@@ -2282,7 +2283,7 @@ LDFLAGS=$ldflags \$(CUSTOMBUILDFLAGS)
+ AMBERLDFLAGS=\$(AMBERBUILDFLAGS)
+ 
+ LEX=   $lex
+-YACC=  \$(BINDIR)/yacc
++YACC=  byacc
+ AR=    ar rv
+ M4=    $m4
+ RANLIB=$ranlib
+@@ -2319,7 +2320,7 @@ CP=$localcp
+ #  Information about Fortran compilation:
+ 
+ FC=$fc
+-FFLAGS= $fflags \$(LOCALFLAGS) \$(CUSTOMBUILDFLAGS) -I\$(INCDIR) \$(NETCDFINC) $mklinc
++FFLAGS= $fflags \$(LOCALFLAGS) \$(CUSTOMBUILDFLAGS) -IGENTOO_INCLUDE \$(NETCDFINC) $mklinc
+ FNOOPTFLAGS= $fnooptflags
+ FOPTFLAGS= $foptflags
+ AMBERFFLAGS=\$(AMBERBUILDFLAGS)
+diff --git a/AmberTools/src/cpptraj/src/Makefile_at b/AmberTools/src/cpptraj/src/Makefile_at
+index 822b451..0684b0c 100644
+--- a/AmberTools/src/cpptraj/src/Makefile_at
++++ b/AmberTools/src/cpptraj/src/Makefile_at
+@@ -29,22 +29,10 @@ dependclean:
+ 	-/bin/rm FindDepend.o
+ 	-/bin/rm findDepend
+ 
+-cpptraj$(SFX): $(NETCDF) $(OBJECTS) $(PTRAJ_OBJECTS) $(EXTERNAL_LIBS) 
++cpptraj$(SFX): $(OBJECTS) $(PTRAJ_OBJECTS)
+ 	$(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(PTRAJ_OBJECTS) \
+                -L$(LIBDIR) $(NETCDFLIB) $(ZLIB) $(BZLIB) $(FLIBS_PTRAJ)
+ 
+-$(INCDIR)/netcdf.mod: ../../netcdf_config.log
+-	cd ../../netcdf/src && $(MAKE) install
+-
+-$(LIBDIR)/libarpack.a:
+-	cd ../../arpack && $(MAKE) install
+-
+-$(LIBDIR)/liblapack.a:
+-	cd ../../lapack && $(MAKE) $(LAPACK)
+-
+-$(LIBDIR)/libblas.a:
+-	cd ../../blas && $(MAKE) $(BLAS)
+-
+ thermo.o:  ../../ptraj/thermo.F90
+ 	$(FC) $(FPPFLAGS) -c $(FREEFORMAT_FLAG) $(FOPTFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ ../../ptraj/thermo.F90
+ 
+diff --git a/AmberTools/src/mdgx/Makefile b/AmberTools/src/mdgx/Makefile
+index 7bad950..b7a560b 100644
+--- a/AmberTools/src/mdgx/Makefile
++++ b/AmberTools/src/mdgx/Makefile
+@@ -132,19 +132,16 @@ MDGX_HEADERS = \
+ 	       ptrajmask.h \
+ 	       ../sff/AmberNetcdf.h 
+ 
+-mdgx$(SFX) : $(MDGX_OBJS) $(LIBDIR)/libfftw3.a
++mdgx$(SFX) : $(MDGX_OBJS)
+ 	$(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) \
+ 	-o $@ $(MDGX_OBJS) $(FFTWLIB) -L$(LIBDIR) $(NETCDFLIB) $(LM)
+ 
+-mdgx.MPI$(SFX) : $(MDGX_OBJS) $(LIBDIR)/libfftw3.a
++mdgx.MPI$(SFX) : $(MDGX_OBJS)
+ 	$(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) \
+ 	-o $@ $(MDGX_OBJS) $(FFTWLIB) -L$(LIBDIR) $(NETCDFLIB) $(LM)
+ 
+-$(LIBDIR)/fftw3.a: ../fftw-3.3/config.log
+-	cd ../fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install;
+-
+ .c.o:
+-	$(CC) -c $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) -I$(INCDIR) -I../fftw-3.3/api -o $@ $<
++	$(CC) -c $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) -I$(INCDIR) -o $@ $<
+ 
+ clean:
+ 	/bin/rm -f $(MDGX_OBJS) mdgx$(SFX)
+diff --git a/AmberTools/src/mdgx/Trajectory.c b/AmberTools/src/mdgx/Trajectory.c
+index 524dad8..5df64c6 100644
+--- a/AmberTools/src/mdgx/Trajectory.c
++++ b/AmberTools/src/mdgx/Trajectory.c
+@@ -214,7 +214,7 @@ void ExtendCoordinates(coord *tc, prmtop *tp)
+ coord ReadRst(prmtop *tp, char* source)
+ {
+   int i, rsttype;
+-  char line[128];
++  char line[MAXLINE];
+   FILE *inp;
+   coord tc;
+ 
+diff --git a/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py b/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py
+index b01b891..24ea20f 100644
+--- a/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py
++++ b/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py
+@@ -210,7 +210,7 @@ class AmberOutput(object):
+ 
+       # write out each frame
+       for i in range(len(self.data[print_keys[0]])):
+-         csvwriter.writerow([i] + [self.data[key][i] for key in print_keys])
++         csvwriter.writerow([i] + ["%.4f" % self.data[key][i] for key in print_keys])
+ 
+    #==================================================
+ 
+@@ -1003,7 +1003,7 @@ class BindingStatistics(object):
+ 
+          # write out each frame
+          for i in range(len(self.data[print_keys[0]])):
+-            csvwriter.writerow([i]+[self.data[key][i] for key in print_keys])
++            csvwriter.writerow([i]+["%.4f" % self.data[key][i] for key in print_keys])
+          csvwriter.writerow([])
+ 
+    #==================================================
+diff --git a/AmberTools/src/nab/database.c b/AmberTools/src/nab/database.c
+index 0b98d35..9aad62a 100644
+--- a/AmberTools/src/nab/database.c
++++ b/AmberTools/src/nab/database.c
+@@ -1135,7 +1135,7 @@ int*		iPLines;
+ char*           PBuffer;
+ int             iBufferInc;
+ {
+-String          sLine;
++String          sLine[MAXDATALINELEN];
+ 
+ 
+ 
+diff --git a/AmberTools/src/nab/nab.c b/AmberTools/src/nab/nab.c
+index 84e03ef..d49b711 100644
+--- a/AmberTools/src/nab/nab.c
++++ b/AmberTools/src/nab/nab.c
+@@ -161,8 +161,8 @@ char	*cppstring;
+                fprintf( stderr, "AMBERHOME is not set!\n" );
+                exit(1);
+             }
+-			sprintf( cmd, "%s/bin/%s %s -I%s/include %s ",
+-				amberhome, CPP, cppstring, amberhome,
++			sprintf( cmd, "%s %s -I%s/include %s ",
++				CPP, cppstring, amberhome,
+ 				argv[ ac ] ? argv[ ac ] : "" );
+ 			if( cgdopt ) fprintf( stderr, "cpp cmd: %s\n", cmd );
+ 			nfields = split( cmd, fields, " " );
+diff --git a/AmberTools/src/pbsa/Makefile b/AmberTools/src/pbsa/Makefile
+index 0a3f12f..2105b00 100644
+--- a/AmberTools/src/pbsa/Makefile
++++ b/AmberTools/src/pbsa/Makefile
+@@ -144,23 +144,23 @@ configured_parallel: configured
+ 	)
+ 
+ #---------------------------------------------------------------------------
+-pbsa$(SFX): FFTW3 $(OBJ) syslib netlib c9x-complex configured_serial 
++pbsa$(SFX): $(OBJ) syslib configured_serial 
+ 	$(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o pbsa$(SFX) $(OBJ) \
+ 	        ../lib/nxtsec.o ../lib/random.o $(FLIBS_FFTW3) \
+ 	        -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
+ 
+-pbsa.MPI$(SFX): FFTW3.MPI $(OBJ) syslib netlib c9x-complex configured_parallel 
++pbsa.MPI$(SFX): $(OBJ) syslib configured_parallel 
+ 	$(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o pbsa.MPI$(SFX) $(OBJ) \
+ 	        ../lib/nxtsec.o ../lib/random.o $(FLIBS_FFTW3) \
+ 	        -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
+ 
+-simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9x-complex
++simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib
+ 	$(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o simplepbsa$(SFX) simplepbsa.o gopt.o \
+ 		libpbsa.a $(LIBDIR)/libsff.a ../lib/nxtsec.o -L$(LIBDIR) $(FLIBSF) \
+ 		$(LDFLAGS) $(AMBERLDFLAGS)
+ 	/bin/mv simplepbsa$(SFX) $(BINDIR)
+ 
+-libpbsa.a: FFTW3 $(LIBPBSAOBJS) syslib
++libpbsa.a: $(LIBPBSAOBJS) syslib
+ 	-rm -f libpbsa.a
+ 	$(AR) libpbsa.a $(LIBPBSAOBJS) ../lib/random.o
+ 	$(RANLIB) libpbsa.a
+@@ -188,48 +188,12 @@ libFpbsa.parallel: $(SANDERPBSAOBJS)
+ 	$(RANLIB) libFpbsa.a
+ 	/bin/mv libFpbsa.a $(LIBDIR)
+ 
+-FFTW3:
+-	@if [ "$(PBSAFLAG)" = "-DFFTW" ]; then \
+-	if [ "$(FLIBS_FFTW3)" = '-lfftw3xf_$(COMPILER)' ]; then\
+-		cd $(MKL)/interfaces/fftw3xf && $(MAKE) lib$(MKL_PROCESSOR) \
+-		compiler=$(COMPILER) PRECISION=MKL_DOUBLE \
+-		INSTALL_DIR=$(LIBDIR); \
+-	else \
+-	    if [ ! -f $(INCDIR)/fftw3.f03 ]; then\
+-		cd ../fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install; \
+-	    fi \
+-	fi \
+-	fi
+-
+-FFTW3.MPI:
+-	@if [ "$(PBSAFLAG)" = "-DFFTW" ]; then \
+-	if [ "$(FLIBS_FFTW3)" = '-lfftw3xf_$(COMPILER)' ]; then\
+-		cd $(MKL)/interfaces/fftw3xf && $(MAKE) lib$(MKL_PROCESSOR) \
+-		compiler=$(COMPILER) PRECISION=MKL_DOUBLE \
+-		INSTALL_DIR=$(LIBDIR); \
+-	else \
+-	    if [ ! -f $(INCDIR)/fftw3-mpi.f03 ]; then\
+-		cd ../fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install; \
+-	    fi \
+-	fi \
+-	fi
+-
+ syslib:
+ 	cd ../lib && $(MAKE) nxtsec.o random.o
+ 
+ sfflib:
+ 	cd ../sff && $(MAKE) install
+ 
+-netlib: 
+-	cd ../lapack && $(MAKE) $(LAPACK)
+-	cd ../blas && $(MAKE) $(BLAS)
+-	cd ../arpack && $(MAKE) install
+-
+-c9x-complex:
+-	@if test $(C9XCOMPLEX) != "skip"; then \
+-	   cd ../c9x-complex && $(MAKE) libmc.a; \
+-	 fi
+-
+ pb_init.o: pb_init.F90
+ 	$(FC) $(PBSAFLAG) $(FPPFLAGS) -c -O0 $(FFLAGS) $(AMBERFFLAGS) -o $@ $<
+ 
+diff --git a/AmberTools/src/ptraj/Makefile b/AmberTools/src/ptraj/Makefile
+index 3e643b9..b3089f1 100644
+--- a/AmberTools/src/ptraj/Makefile
++++ b/AmberTools/src/ptraj/Makefile
+@@ -61,21 +61,16 @@ rdparm$(SFX): libs $(OBJECTS)
+ 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
+ 		-o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
+ 
+-ptraj$(SFX): libs netlib $(OBJECTS)
++ptraj$(SFX): libs $(OBJECTS)
+ 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
+ 		-o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
+ 
+-ptraj.MPI$(SFX): libs netlib $(OBJECTS)
++ptraj.MPI$(SFX): libs $(OBJECTS)
+ 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
+ 		-o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $(LM)
+ 
+ libs: 
+ 	cd pdb && $(MAKE) 
+-	cd ../arpack && $(MAKE)
+-
+-netlib:
+-	cd ../lapack && $(MAKE) $(LAPACK)
+-	cd ../blas && $(MAKE) $(BLAS)
+ 
+ clean:
+ 	cd pdb && $(MAKE) clean
+diff --git a/AmberTools/src/ptraj/trajectory.c b/AmberTools/src/ptraj/trajectory.c
+index 110ffce..49bdf1a 100644
+--- a/AmberTools/src/ptraj/trajectory.c
++++ b/AmberTools/src/ptraj/trajectory.c
+@@ -1315,7 +1315,7 @@ readAmberTrajectory_nobuffer(FILE *fpin, int natoms,
+ {
+   fpos_t fileMarker;         /* marker for current file postition */
+   char *junk;
+-  char buffer[120];
++  char buffer[BUFFER_SIZE];
+   char coords[26];    /* room for 24 characters (3f8.3) + \n + (char) 0  */
+   char c;     
+   int j,ret;
+diff --git a/AmberTools/src/sff/Makefile b/AmberTools/src/sff/Makefile
+index 83f362c..b1a1b2e 100644
+--- a/AmberTools/src/sff/Makefile
++++ b/AmberTools/src/sff/Makefile
+@@ -3,7 +3,7 @@ include ../config.h
+ .c.o:
+ 	$(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) $(NETCDFINC) -o $@ $<
+ 
+-OBJS = binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o nmode.o \
++OBJS = binpos.o conjgrad.o dsarpack.o lmodC.o memutil.o nblist.o newton.o nmode.o \
+ 	prm.o rand2.o sasad.o sff.o time.o xminC.o AmberNetcdf.o $(SFF_RISM_INTERFACE)
+ 
+ 
+diff --git a/AmberTools/src/sff/dsarpack.f b/AmberTools/src/sff/dsarpack.f
+index e69de29..5544df9 100644
+--- a/AmberTools/src/sff/dsarpack.f
++++ b/AmberTools/src/sff/dsarpack.f
+@@ -0,0 +1,654 @@
++      subroutine dsarpack(n_dim,n_eig_in,n_eig_out,ncv_in,itr_in,
++     &                    eigval_tol,eigvals,eigvecs,spectrum,
++     &                    need_eigvecs,ierr,debug_arpack,
++     &                    v,workl,workd,d,resid,ax,select,
++     &                    xyz,grad,return_flag,label)
++c
++      implicit none
++c
++c     %-----------------%
++c     | Dummy Arguments |
++c     %-----------------%
++c
++      integer n_dim,n_eig_in,n_eig_out,ncv_in,itr_in,spectrum,
++     &        need_eigvecs,ierr,debug_arpack,return_flag,label
++      Double precision eigval_tol
++      Double precision eigvals(n_eig_in),eigvecs(n_dim * n_eig_in)
++      Double precision v(n_dim,ncv_in),
++     &                 workl(ncv_in*(ncv_in+8)),workd(3*n_dim),
++     &                 d(ncv_in,2),resid(n_dim),ax(n_dim),
++     &                 xyz(n_dim),grad(n_dim)
++      logical select(ncv_in)
++c
++      save
++c
++c     %---------------%
++c     | Include Files |
++c     %---------------%
++c
++c     include 'debug.h'
++c
++c\SCCS Information: @(#) 
++c FILE: debug.h   SID: 2.3   DATE OF SID: 11/16/95   RELEASE: 2 
++c
++c     %---------------------------------%
++c     | See debug.doc for documentation |
++c     %---------------------------------%
++      integer  logfil, ndigit, mgetv0,
++     &         msaupd, msaup2, msaitr, mseigt, msapps, msgets, mseupd,
++     &         mnaupd, mnaup2, mnaitr, mneigh, mnapps, mngets, mneupd,
++     &         mcaupd, mcaup2, mcaitr, mceigh, mcapps, mcgets, mceupd
++      common /debug/ 
++     &         logfil, ndigit, mgetv0,
++     &         msaupd, msaup2, msaitr, mseigt, msapps, msgets, mseupd,
++     &         mnaupd, mnaup2, mnaitr, mneigh, mnapps, mngets, mneupd,
++     &         mcaupd, mcaup2, mcaitr, mceigh, mcapps, mcgets, mceupd
++c
++c     This code shows how to use ARPACK to find a few eigenvalues 
++c     (lambda) and corresponding eigenvectors (x) for the standard 
++c     eigenvalue problem:
++c          
++c                        A*x = lambda*x
++c 
++c     where A is an n by n real symmetric matrix.
++c
++c     The main points illustrated here are 
++c
++c        1) How to declare sufficient memory to find NEV 
++c           eigenvalues of largest magnitude.  Other options
++c           are available.
++c
++c        2) Illustration of the reverse communication interface 
++c           needed to utilize the top level ARPACK routine DSAUPD 
++c           that computes the quantities needed to construct
++c           the desired eigenvalues and eigenvectors(if requested).
++c
++c        3) How to extract the desired eigenvalues and eigenvectors
++c           using the ARPACK routine DSEUPD.
++c
++c     The only thing that must be supplied in order to use this
++c     routine on your problem is to change the array dimensions 
++c     appropriately, to specify WHICH eigenvalues you want to compute 
++c     and to supply a matrix-vector product
++c
++c                         w <-  Av
++c
++c     in place of the call to AV( ) below.
++c
++c     Once usage of this routine is understood, you may wish to explore
++c     the other available options to improve convergence, to solve generalized
++c     problems, etc.  Look at the file ex-sym.doc in DOCUMENTS directory.
++c     This codes implements  
++c
++c\Example-1
++c     ... Suppose we want to solve A*x = lambda*x in regular mode,
++c         where A is derived from the central difference discretization
++c         of the 2-dimensional Laplacian on the unit square with
++c         zero Dirichlet boundary condition.
++c     ... OP = A  and  B = I.
++c     ... Assume "call av (n,x,y)" computes y = A*x
++c     ... Use mode 1 of DSAUPD.
++c
++c\BeginLib
++c
++c\Routines called:
++c     dsaupd  ARPACK reverse communication interface routine.
++c     dseupd  ARPACK routine that returns Ritz values and (optionally)
++c             Ritz vectors.
++c     dnrm2   Level 1 BLAS that computes the norm of a vector.
++c     daxpy   Level 1 BLAS that computes y <- alpha*x+y.
++c
++c\Author
++c     Richard Lehoucq
++c     Danny Sorensen
++c     Chao Yang
++c     Dept. of Computational &
++c     Applied Mathematics
++c     Rice University
++c     Houston, Texas
++c
++c\SCCS Information: %Z%
++c FILE: %M%   SID: %I%   DATE OF SID: %G%   RELEASE: %R%
++c
++c\Remarks
++c     1. None
++c
++c\EndLib
++c
++c-----------------------------------------------------------------------
++c
++c     %-------------------------------------------------------%
++c     | Storage Declarations:                                 |
++c     |                                                       |
++c     | The maximum dimensions for all arrays are             |
++c     | set here to accommodate a problem size of             |
++c     | N .le. MAXN                                           |
++c     |                                                       |
++c     | NEV is the number of eigenvalues requested.           |
++c     |     See specifications for ARPACK usage below.        |
++c     |                                                       |
++c     | NCV is the largest number of basis vectors that will  |
++c     |     be used in the Implicitly Restarted Arnoldi       |
++c     |     Process.  Work per major iteration is             |
++c     |     proportional to N*NCV*NCV.                        |
++c     |                                                       |
++c     | You must set:                                         |
++c     |                                                       |
++c     | MAXN:   Maximum dimension of the A allowed. (dynamic) |
++c     | MAXNEV: Maximum NEV allowed. (dynamic)                |
++c     | MAXNCV: Maximum NCV allowed. (dynamic)                |
++c     %-------------------------------------------------------%
++c
++C     %--------------------------------------%
++C     | F90 Allocatable Arrays (on the heap) |
++C     %--------------------------------------%
++c
++C     Double precision,allocatable,save :: v(:,:)
++C     integer,save :: v_row_allocated = 0, v_col_allocated = 0
++c
++c     %----------------------------------------------%
++c     | Originally, as F77 parameters, the following |
++c     | integers were used to dimension work arrays. |
++c     | They are replaced by dummy arguments used to |
++c     | dimension the work arrays as F90 automatic   |
++c     | arrays, but the integers are still used for  |
++c     | passing the dimensions to lower level ARPACK |
++c     | routines dsaupd, dseupd and dmout.           |
++c     %----------------------------------------------%
++c
++      integer          maxn, maxnev, maxncv, ldv
++c
++c     %-------------------------------------------%
++c     | Local F90 Automatic Arrays (on the stack) |
++c     %-------------------------------------------%
++c
++      Double precision
++C    &                 workl(ncv_in*(ncv_in+8)),
++C    &                 workd(3*n_dim), d(ncv_in,2), resid(n_dim),
++C    &                 ax(n_dim),
++     &                 cg_dstat(4)
++C     logical          select(ncv_in)
++      integer          iparam(11), ipntr(11),
++     &                 cg_istat(4)
++c
++c     %---------------%
++c     | Local Scalars |
++c     %---------------%
++c
++      character        bmat*1, which*2
++      integer          ido, n, nev, ncv, lworkl, info,
++     &                 i, j, nx, ishfts, maxitr, mode1, nconv
++      integer          L12, L18, ARPACK_ERROR, status_flag
++      data             L12, L18, ARPACK_ERROR /1, 2, -2/
++C     integer          v_row_needed, v_col_needed
++      logical          rvec
++      Double precision      
++     &                 tol, sigma
++c
++c     %------------%
++c     | Parameters |
++c     %------------%
++c
++      Double precision
++     &                 zero
++      parameter        (zero = 0.0D+0)
++c  
++c     %-----------------------------%
++c     | BLAS & LAPACK routines used |
++c     %-----------------------------%
++c
++      Double precision           
++     &                 dnrm2
++      external         dnrm2, daxpy, hessvec
++c
++c     %--------------------%
++c     | Intrinsic function |
++c     %--------------------%
++c
++      intrinsic        abs
++c
++c     %-----------------------%
++c     | Executable Statements |
++c     %-----------------------%
++c
++      if ( label.eq.0 ) go to 1
++      go to (12,18) label
++  1   continue
++c
++c     %------------------------------------------------%
++c     | Values used to calculate work array dimensions |
++c     %------------------------------------------------%
++c
++      maxn = n_dim
++      maxnev = n_eig_in
++      maxncv = ncv_in
++      ldv = maxn
++c
++c     %---------------------------------------------------%
++c     | The include debug.h statement above and           |
++c     | assignments here initiate trace output from the   |
++c     | internal actions of ARPACK.  See debug.doc in the |
++c     | DOCUMENTS directory for usage.  Initially, the    |
++c     | most useful information will be a breakdown of    |
++c     | time spent in the various stages of computation   |
++c     | given by setting msaupd = 1.                      |
++c     %---------------------------------------------------%
++c
++      ndigit = -5
++      logfil = 6
++      msgets = 0
++      msaitr = 0 
++      msapps = 0
++      if ( debug_arpack.eq.1 ) then
++        msaupd = 1
++      else
++        msaupd = 0
++      endif
++      msaup2 = 0
++      mseigt = 0
++      mseupd = 0
++c     
++c   *** Allocatable array v will be allowed to grow to its largest size;
++c   ***  it is never deallocated:
++C     v_row_needed = n_dim        !!! ldv
++C     v_col_needed = ncv_in       !!! maxncv
++C     if( allocated(v) )then
++C       if( (v_row_needed .gt. v_row_allocated)
++C    & .or. (v_col_needed .gt. v_col_allocated) )then
++C         deallocate(v,stat=ierr)
++C         if( ierr .ne. 0 )then
++C           write( logfil, '(a,i16,1x,i8)' )
++C    &       'ARPACK: could not deallocate v'
++C           go to 9000
++C         endif
++C       endif
++C     endif
++C     if( .not. allocated(v) )then
++C       allocate( v(v_row_needed,v_col_needed), stat=ierr )
++C       if( ierr .ne. 0 )then
++C         write( logfil, '(a,2i10)' )
++C    &     'ARPACK: could not allocate v'
++C         go to 9000
++C       endif
++C       v_row_allocated = v_row_needed
++C       v_col_allocated = v_col_needed
++C     endif
++C     v = zero !!! zero out entire v array
++c     
++c     %-------------------------------------------------%
++c     | The following sets dimensions for this problem. |
++c     %-------------------------------------------------%
++c
++      n = n_dim
++c
++c     %----------------------------------------------%
++c     |                                              | 
++c     | Specifications for ARPACK usage are set      | 
++c     | below:                                       |
++c     |                                              |
++c     |    1) NEV = N_EIG_IN  asks for N_EIG_IN      |  
++c     |       eigenvalues to be computed.            | 
++c     |                                              |
++c     |    2) NCV = NCV_IN sets the length of the    |
++c     |       Arnoldi factorization                  |
++c     |                                              |
++c     |    3) This is a standard problem             |
++c     |         (indicated by bmat  = 'I')           |
++c     |                                              |
++c     |    4) Ask for the NEV eigenvalues of         |
++c     |       smallest magnitude                     |
++c     |         (indicated by which = 'SM')          |
++c     |       See documentation in SSAUPD for the    |
++c     |       other options SA, LA, LM, BE.          | 
++c     |                                              |
++c     | Note: NEV and NCV must satisfy the following |
++c     | conditions:                                  |
++c     |              NEV <= MAXNEV                   |
++c     |          NEV + 1 <= NCV <= MAXNCV            |
++c     %----------------------------------------------%
++c
++      nev   = n_eig_in
++      ncv   = ncv_in 
++      bmat  = 'I'
++      if ( spectrum .eq. 1 ) then
++         which = 'SM'
++      else if ( spectrum .eq. 2 ) then
++         which = 'SA'
++      else if ( spectrum .eq. 3 ) then
++         which = 'LM'
++      else if ( spectrum .eq. 4 ) then
++         which = 'LA'
++      else if ( spectrum .eq. 5 ) then
++         which = 'BE'
++      else
++          print *, ' ERROR with _SSIMP: Spectrum .NE. (SM|SA|LA|LM|BE)'
++         go to 9000
++      end if
++c
++      if ( n .gt. maxn ) then
++         print *, ' ERROR with _SSIMP: N is greater than MAXN '
++         go to 9000
++      else if ( nev .gt. maxnev ) then
++         print *, ' ERROR with _SSIMP: NEV is greater than MAXNEV '
++         go to 9000
++      else if ( ncv .gt. maxncv ) then
++         print *, ' ERROR with _SSIMP: NCV is greater than MAXNCV '
++         go to 9000
++      end if
++c
++c     %-----------------------------------------------------%
++c     |                                                     |
++c     | Specification of stopping rules and initial         |
++c     | conditions before calling DSAUPD                    |
++c     |                                                     |
++c     | TOL  determines the stopping criterion.             |
++c     |                                                     |
++c     |      Expect                                         |
++c     |           abs(lambdaC - lambdaT) < TOL*abs(lambdaC) |
++c     |               computed   true                       |
++c     |                                                     |
++c     |      If TOL .le. 0,  then TOL <- macheps            |
++c     |           (machine precision) is used.              |
++c     |                                                     |
++c     | IDO  is the REVERSE COMMUNICATION parameter         |
++c     |      used to specify actions to be taken on return  |
++c     |      from DSAUPD. (See usage below.)                |
++c     |                                                     |
++c     |      It MUST initially be set to 0 before the first |
++c     |      call to DSAUPD.                                | 
++c     |                                                     |
++c     | INFO on entry specifies starting vector information |
++c     |      and on return indicates error codes            |
++c     |                                                     |
++c     |      Initially, setting INFO=0 indicates that a     | 
++c     |      random starting vector is requested to         |
++c     |      start the ARNOLDI iteration.  Setting INFO to  |
++c     |      a nonzero value on the initial call is used    |
++c     |      if you want to specify your own starting       |
++c     |      vector (This vector must be placed in RESID.)  | 
++c     |                                                     |
++c     | The work array WORKL is used in DSAUPD as           | 
++c     | workspace.  Its dimension LWORKL is set as          |
++c     | illustrated below.                                  |
++c     |                                                     |
++c     %-----------------------------------------------------%
++c
++      lworkl = ncv*(ncv+8)
++      tol = eigval_tol 
++      info = 0
++      ido = 0
++c
++c     %---------------------------------------------------%
++c     | Specification of Algorithm Mode:                  |
++c     |                                                   |
++c     | This program uses the exact shift strategy        |
++c     | (indicated by setting PARAM(1) = 1).              |
++c     | IPARAM(3) specifies the maximum number of Arnoldi |
++c     | iterations allowed.  Mode 1 of DSAUPD is used     |
++c     | (IPARAM(7) = 1). All these options can be changed |
++c     | by the user. For details see the documentation in |
++c     | DSAUPD.                                           |
++c     %---------------------------------------------------%
++c
++      ishfts = 1
++      maxitr = itr_in 
++      mode1 = 1
++c
++      iparam(1) = ishfts
++c                
++      iparam(3) = maxitr
++c                  
++      iparam(7) = mode1
++c
++c     %------------------------------------------------%
++c     | M A I N   L O O P (Reverse communication loop) |
++c     %------------------------------------------------%
++c
++ 10   continue
++c
++c        %---------------------------------------------%
++c        | Repeatedly call the routine DSAUPD and take | 
++c        | actions indicated by parameter IDO until    |
++c        | either convergence is indicated or maxitr   |
++c        | has been exceeded.                          |
++c        %---------------------------------------------%
++c
++         call dsaupd ( ido, bmat, n, which, nev, tol, resid, 
++     &                 ncv, v, ldv, iparam, ipntr, workd, workl,
++     &                 lworkl, info )
++c
++         if (ido .eq. -1 .or. ido .eq. 1) then
++c
++c           %--------------------------------------%
++c           | Perform matrix vector multiplication |
++c           |              y <--- OP*x             |
++c           | The user should supply his/her own   |
++c           | matrix vector multiplication routine |
++c           | here that takes workd(ipntr(1)) as   |
++c           | the input, and return the result to  |
++c           | workd(ipntr(2)).                     |
++c           %--------------------------------------%
++c
++            status_flag = 0
++ 11         continue
++               call hessvec ( n, workd(ipntr(1)), workd(ipntr(2)),
++     &                        xyz, grad, return_flag, status_flag )
++               if ( status_flag.eq.0 ) go to 13
++               if ( status_flag.lt.0 ) go to 9000
++               label = L12
++               return
++ 12         go to 11
++ 13         continue
++c
++c           %-----------------------------------------%
++c           | L O O P   B A C K to call DSAUPD again. |
++c           %-----------------------------------------%
++c
++            go to 10
++c
++         end if 
++c
++c     %----------------------------------------%
++c     | Either we have convergence or there is |
++c     | an error.                              |
++c     %----------------------------------------%
++c
++      if ( info .lt. 0 ) then
++c
++c        %--------------------------%
++c        | Error message. Check the |
++c        | documentation in DSAUPD. |
++c        %--------------------------%
++c
++         print *, ' '
++         print *, ' Error with _saupd, info = ', info
++         print *, ' Check documentation in _saupd '
++         print *, ' '
++         go to 9000
++c
++      else 
++c
++c        %-------------------------------------------%
++c        | No fatal errors occurred.                 |
++c        | Post-Process using DSEUPD.                |
++c        |                                           |
++c        | Computed eigenvalues may be extracted.    |  
++c        |                                           |
++c        | Eigenvectors may be also computed now if  |
++c        | desired.  (indicated by rvec = .true.)    | 
++c        |                                           |
++c        | The routine DSEUPD now called to do this  |
++c        | post processing (Other modes may require  |
++c        | more complicated post processing than     |
++c        | mode1.)                                   |
++c        |                                           |
++c        %-------------------------------------------%
++c           
++         if ( need_eigvecs .eq. 1 ) then
++            rvec = .true.
++         else
++            rvec = .false.
++         end if
++c
++         call dseupd ( rvec, 'All', select, d, v, ldv, sigma, 
++     &        bmat, n, which, nev, tol, resid, ncv, v, ldv, 
++     &        iparam, ipntr, workd, workl, lworkl, ierr )
++c
++c        %----------------------------------------------%
++c        | Eigenvalues are returned in the first column |
++c        | of the two dimensional array D and the       |
++c        | corresponding eigenvectors are returned in   |
++c        | the first NCONV (=IPARAM(5)) columns of the  |
++c        | two dimensional array V if requested.        |
++c        | Otherwise, an orthogonal basis for the       |
++c        | invariant subspace corresponding to the      |
++c        | eigenvalues in D is returned in V.           |
++c        %----------------------------------------------%
++c
++         if ( ierr .ne. 0) then
++c
++c           %------------------------------------%
++c           | Error condition:                   |
++c           | Check the documentation of DSEUPD. |
++c           %------------------------------------%
++c
++            print *, ' '
++            print *, ' Error with _seupd, info = ', ierr
++            print *, ' Check the documentation of _seupd. '
++            print *, ' '
++            go to 9000
++c
++         else if ( debug_arpack.eq.1 ) then
++c
++            nconv =  iparam(5)
++            n_eig_out = nconv
++            if ( nconv .le. 0 ) then
++               print *, ' '
++               print *, ' ARPACK: Not a single mode converged.'
++               print *, ' '
++               go to 9000
++            endif
++c
++C           %--------------------------------------------%
++C           | "UnDO" DO 20 j=1,nconv loop, because it is |
++C           | illegal to jump in and out from a DO loop. |
++C           %--------------------------------------------%
++c
++            j = 1
++ 16         continue
++c
++c              %---------------------------%
++c              | Compute the residual norm |
++c              |                           |
++c              |   ||  A*x - lambda*x ||   |
++c              |                           |
++c              | for the NCONV accurately  |
++c              | computed eigenvalues and  |
++c              | eigenvectors.  (iparam(5) |
++c              | indicates how many are    |
++c              | accurate to the requested |
++c              | tolerance)                |
++c              %---------------------------%
++c
++               status_flag = 0
++ 17            continue
++                  call hessvec ( n, v(1,j), ax, xyz, grad,
++     &                           return_flag, status_flag )
++                  if ( status_flag.eq.0 ) go to 19
++                  if ( status_flag.lt.0 ) go to 9000
++                  label = L18
++                  return
++ 18            go to 17
++ 19            continue
++c
++               call daxpy(n, -d(j,1), v(1,j), 1, ax, 1)
++               d(j,2) = dnrm2(n, ax, 1)
++               d(j,2) = d(j,2) / abs(d(j,1))
++c
++               j = j + 1
++               if ( j .gt. nconv ) go to 20
++c
++               go to 16
++c
++ 20         continue
++c
++c           %-----------------------------%
++c           | Display computed residuals. |
++c           %-----------------------------%
++c
++            call dmout(6, nconv, 2, d, maxncv, -6,
++     &           'Ritz values and relative residuals')
++c
++c           %-------------------------------------------%
++c           | Print additional convergence information. |
++c           %-------------------------------------------%
++c
++            if ( info .eq. 1) then
++               print *, ' '
++               print *, ' Maximum number of iterations reached.'
++               print *, ' '
++            else if ( info .eq. 3) then
++               print *, ' '
++               print *, ' No shifts could be applied during implicit',
++     &                  ' Arnoldi update, try increasing NCV.'
++               print *, ' '
++            end if
++c
++            print *, ' '
++            print *, ' _SSIMP '
++            print *, ' ====== '
++            print *, ' '
++            print *, ' Size of the matrix is ', n
++            print *, ' The number of Ritz values requested is ', nev
++            print *, ' The number of Arnoldi vectors generated',
++     &               ' (NCV) is ', ncv
++            print *, ' What portion of the spectrum: ', which
++            print *, ' The number of converged Ritz values is ',
++     &                 nconv
++            print *, ' The number of Implicit Arnoldi update',
++     &               ' iterations taken is ', iparam(3)
++            print *, ' The number of OP*x is ', iparam(9)
++            print *, ' The convergence criterion is ', tol
++            print *, ' '
++         end if
++c
++c        %----------------------------%
++c        | Return eigvals and eigvecs |
++c        %----------------------------%
++c
++         nconv =  iparam(5)
++         n_eig_out = nconv
++         if ( nconv .le. 0 ) then
++            print *, ' '
++            print *, ' ARPACK: Not a single mode converged.'
++            print *, ' '
++            go to 9000
++         endif
++c
++         do 40 j=1, nconv
++             eigvals(j) = d(j,1)
++c
++             do 30 i=1, n
++                eigvecs((j-1)*n+i) = v(i,j)
++ 30          continue
++ 40      continue
++c
++      end if
++c
++c     %--------------------------------%
++c     | Done with subroutine dsarpack. |
++c     %--------------------------------%
++c
++      label = 0
++      return
++c
++ 9000 continue !!! Error
++c
++      if( status_flag.eq.0 ) status_flag = ARPACK_ERROR
++c
++      label = status_flag
++      return
++c
++      end
++c 
++c ------------------------------------------------------------------
+diff --git a/AmberTools/src/sqm/Makefile b/AmberTools/src/sqm/Makefile
+index 3b49c55..61d0dc3 100644
+--- a/AmberTools/src/sqm/Makefile
++++ b/AmberTools/src/sqm/Makefile
+@@ -82,7 +82,7 @@ QMOBJ = qm2_allocate_e_repul.o qm2_calc_charges.o qm2_calc_dipole.o \
+ install: sqm$(SFX)
+ 	mv sqm$(SFX) $(BINDIR)
+ 
+-sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys
++sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys
+ 	$(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) \
+ 		-L$(LIBDIR) $(FLIBSF) ../lib/sys.a $(LDFLAGS) $(AMBERLDFLAGS)
+ 
+@@ -101,11 +101,6 @@ $(LIBDIR)/libsqm.a: $(QMOBJ) $(LIBQMOBJ)
+ sys:
+ 	cd ../lib; $(MAKE) sys.a
+ 
+-netlib:
+-	cd ../lapack; $(MAKE) $(LAPACK)
+-	cd ../blas; $(MAKE) $(BLAS)
+-	cd ../arpack && $(MAKE) install
+-
+ clean:
+ 	/bin/rm -f *.o  *.mod *.d sqm$(SFX)
+ 
+diff --git a/AmberTools/test/mmpbsa_py/01_Generalized_Born/energies.csv.save b/AmberTools/test/mmpbsa_py/01_Generalized_Born/energies.csv.save
+index 3595375..1a0be46 100644
+--- a/AmberTools/test/mmpbsa_py/01_Generalized_Born/energies.csv.save
++++ b/AmberTools/test/mmpbsa_py/01_Generalized_Born/energies.csv.save
+@@ -7,16 +7,16 @@ Frame #,VDWAALS,EEL,EGB,ESURF,G gas,G solv,TOTAL
+ Receptor Energy Terms

+ Frame #,VDWAALS,EEL,EGB,ESURF,G gas,G solv,TOTAL

+ 0,-1969.4265,-17103.7958,-3027.0953,101.7772,-19073.2223,-2925.3181,-21998.5404

+-1,-1956.6674,-17020.9923,-3062.954,102.3918,-18977.6597,-2960.5622,-21938.2219

++1,-1956.6674,-17020.9923,-3062.9540,102.3918,-18977.6597,-2960.5622,-21938.2219

+ 

+ Ligand Energy Terms

+ Frame #,VDWAALS,EEL,EGB,ESURF,G gas,G solv,TOTAL

+-0,-1.2566,-5.6263,-28.5797,4.4486,-6.8829,-24.1311,-31.014

++0,-1.2566,-5.6263,-28.5797,4.4486,-6.8829,-24.1311,-31.0140

+ 1,-3.1118,-6.1548,-29.3738,4.4016,-9.2666,-24.9722,-34.2388

+ 

+ DELTA Energy Terms

+ Frame #,VDWAALS,EEL,EGB,ESURF,DELTA G gas,DELTA G solv,DELTA TOTAL

+-0,-63.4582,-32.3518,35.2679,-8.3751,-95.81,26.8928,-68.9172

+-1,-60.9966,-35.1045,41.6205,-8.465,-96.1011,33.1555,-62.9456

++0,-63.4582,-32.3518,35.2679,-8.3751,-95.8100,26.8928,-68.9172

++1,-60.9966,-35.1045,41.6205,-8.4650,-96.1011,33.1555,-62.9456

+ 

+ 

+diff --git a/AmberTools/test/nab/Run.rism_sp b/AmberTools/test/nab/Run.rism_sp
+index bd8471d..a88bf58 100755
+--- a/AmberTools/test/nab/Run.rism_sp
++++ b/AmberTools/test/nab/Run.rism_sp
+@@ -47,7 +47,7 @@ $DO_PARALLEL $cmd --pdb ala.pdb --prmtop ala.parm7 --traj ala.nc \
+                   --polarDecomp\
+                   --noprogress > rism3d.snglpnt.out || error
+ 
+-checkrism3d -err 1e-6 rism3d.snglpnt.out.check rism3d.snglpnt.out
++./checkrism3d -err 1e-6 rism3d.snglpnt.out.check rism3d.snglpnt.out
+ 
+ awk '{if (NR % 10 == 0) print $0}' quv.1.xyzv > quv.1.xyzv.trunc
+ ../dacdif -r 1e-6 quv.1.xyzv.trunc.check quv.1.xyzv.trunc
+diff --git a/AmberTools/test/nab/Run.rism_sp2 b/AmberTools/test/nab/Run.rism_sp2
+index a2b9521..11da8de 100755
+--- a/AmberTools/test/nab/Run.rism_sp2
++++ b/AmberTools/test/nab/Run.rism_sp2
+@@ -38,7 +38,7 @@ $DO_PARALLEL $cmd --pdb ala.pdb --prmtop ala.parm7 --traj ala.crd \
+                   --buffer 10 --guv guv.2\
+                   --noprogress > rism3d.snglpnt.2.out || error
+ 
+-checkrism3d -err 1e-6 rism3d.snglpnt.2.out.check rism3d.snglpnt.2.out
++./checkrism3d -err 1e-6 rism3d.snglpnt.2.out.check rism3d.snglpnt.2.out
+ ../dacdif -a 1e-6 guv.2.O.1.dx.check guv.2.O.1.dx
+ ../dacdif -a 1e-6 guv.2.H1.2.dx.check guv.2.H1.2.dx
+ ../dacdif -a 1e-6 guv.2.O.3.dx.check guv.2.O.3.dx