diff options
Diffstat (limited to 'sci-chemistry/ambertools')
14 files changed, 0 insertions, 4531 deletions
diff --git a/sci-chemistry/ambertools/Manifest b/sci-chemistry/ambertools/Manifest deleted file mode 100644 index be7b142b3..000000000 --- a/sci-chemistry/ambertools/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST AmberTools12.tar.bz2 89175545 BLAKE2B cbcdadc0e207606ff4a67e31d715ac4f1113d0d72a6f7b17243d448ced788ab75fd7ed93a299e7be120b15fae187697838d6799db02e8efc25c37c207ae3eaca SHA512 4c34d460fdedf00ade847040856d4bf7df65e7370d4a696dd858fdd3612c192ddc13dabde559bc1a7ae4068ba8040ee159479e247b2c1e59ed976a5aa6344970 -DIST AmberTools15.tar.bz2 231809206 SHA256 f0ed40998d0dc8ce5487aaa673827b8cf29bed2b6a09dbdec22e90236a614ec8 SHA512 f91ec69a0f0c632aea9152d36c63dc1ce67a6aaa7b77715fb3b12cadcbcc687ec2a142bd6a0e600cfb8715ae25c33fe90ad8bee3d5bbe94359e91c9e62c1dbd0 WHIRLPOOL 20565fbf1959ce994c590a9f97818a847974f4fabddf4c1719eb85b4ae39f7f52acd5eaddbb5e2c5871454cede066f0f21a69f01ae0ecba4dee0b45f28dd4437 -DIST ambertools-bugfixes-12_p38.tar.xz 88340 BLAKE2B 2bf4e6159a8ad3b064e4abb42e87b0340030400d79497a998009d9680b2e54816071162ad675c4e08dc12b7ce65e831cf9045a046d6f86282e4752cd796399ee SHA512 485123d81e689e06f2a1affc9f17d99e9ba18f92e464beb8fb9c835897693a1bd7d330a8bf9d3526c91eadb32a9b58692185e218c61002f0eeab22ff6efbbb08 diff --git a/sci-chemistry/ambertools/ambertools-12_p38-r1.ebuild b/sci-chemistry/ambertools/ambertools-12_p38-r1.ebuild deleted file mode 100644 index e8fe18256..000000000 --- a/sci-chemistry/ambertools/ambertools-12_p38-r1.ebuild +++ /dev/null @@ -1,164 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils fortran-2 multilib multiprocessing toolchain-funcs - -DESCRIPTION="A suite for carrying out complete molecular mechanics investigations" -HOMEPAGE="http://ambermd.org/#AmberTools" -SRC_URI=" - AmberTools${PV%_p*}.tar.bz2 - http://dev.gentoo.org/~jlec/distfiles/${PN}-bugfixes-${PV}.tar.xz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux" -IUSE="openmp X" - -RESTRICT="fetch" - -RDEPEND=" - virtual/cblas - virtual/lapack - sci-libs/clapack - sci-libs/arpack - sci-libs/cifparse-obj - sci-chemistry/mopac7 - sci-libs/netcdf - >=sci-libs/fftw-3.3:3.0 - sci-chemistry/reduce" -DEPEND="${RDEPEND} - app-shells/tcsh - dev-util/byacc - dev-libs/libf2c - sys-devel/ucpp" - -S="${WORKDIR}/amber12" - -pkg_nofetch() { - einfo "Go to ${HOMEPAGE} and get AmberTools${PV%_p*}.tar.bz2" - einfo "and download http://dev.gentoo.org/~jlec/distfiles/${PN}-bugfixes-${PV}.tar.xz" - einfo "Place both into ${DISTDIR}" -} - -pkg_setup() { - fortran-2_pkg_setup - if use openmp; then - tc-has-openmp || \ - die "Please select an openmp capable compiler like gcc[openmp]" - fi - export AMBERHOME="${S}" -} - -src_prepare() { - epatch \ - "${FILESDIR}"/${P}-gcc5.patch \ - "${FILESDIR}"/${P}-format-security.patch \ - "${FILESDIR}"/${PN}-12-gentoo.patch \ - "${WORKDIR}"/bugfixes/bugfix.{14..38} - cd "${S}"/AmberTools/src || die - rm -r \ - arpack \ - blas \ - byacc \ - lapack \ - fftw-3.3 \ - c9x-complex \ - cifparse \ - netcdf \ - reduce \ - ucpp-1.3 \ - || die - - cd "${S}"/AmberTools/src || die - sed \ - -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \ - -e "s:\\\\\$(LIBDIR)/lapack.a:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \ - -e "s:-llapack:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \ - -e "s:\\\\\$(LIBDIR)/blas.a:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \ - -e "s:-lblas:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \ - -e "s:GENTOO_CFLAGS:${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:$($(tc-getPKG_CONFIG) fftw3 --libs):" \ - -e "s:fc=g77:fc=$(tc-getFC):g" \ - -e "s:\$netcdfflag:$($(tc-getPKG_CONFIG) netcdf --libs):g" \ - -e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \ - -i configure2 || die - - sed \ - -e "s:arsecond_:arscnd_:g" \ - -i sff/time.c sff/sff.h sff/sff.c || die - -} - -src_configure() { - local myconf="--no-updates" - - use X || myconf="${myconf} -noX11" - - use openmp && myconf="${myconf} -openmp" - - cd "${S}" || die - - sed \ - -e '/patch_amber.py/d' \ - -i configure || die - - ./configure \ - ${myconf} \ - -nobintraj \ - -nomtkpp \ - gnu || die -} - -src_test() { - use openmp && export OMP_NUM_THREADS=$(makeopts_jobs) - - emake test -} - -src_compile() { - emake \ - CC=$(tc-getCC) \ - FC=$(tc-getFC) -} - -src_install() { - rm bin/*.py || die - - 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" || die - for x in *; do - dosym ../../../bin/${x} /usr/share/${PN}/bin/${x} - done - cd "${S}" || die - - dodoc doc/AmberTools12.pdf - dolib.a lib/* - insinto /usr/include/${PN} - doins include/* - insinto /usr/share/${PN} - doins -r dat - cd AmberTools || die - doins -r benchmarks examples test - - cat >> "${T}"/99ambertools <<- EOF - AMBERHOME="${EPREFIX}/usr/share/ambertools" - EOF - doenvd "${T}"/99ambertools -} diff --git a/sci-chemistry/ambertools/ambertools-15_p6.ebuild b/sci-chemistry/ambertools/ambertools-15_p6.ebuild deleted file mode 100644 index 8aa759071..000000000 --- a/sci-chemistry/ambertools/ambertools-15_p6.ebuild +++ /dev/null @@ -1,190 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit fortran-2 python-r1 toolchain-funcs - -DESCRIPTION="A suite for carrying out complete molecular mechanics investigations" -HOMEPAGE="http://ambermd.org/#AmberTools" -SRC_URI=" - AmberTools${PV%_p*}.tar.bz2" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux" -IUSE="X" - -RESTRICT="fetch" - -RDEPEND="${PYTHON_DEPS} - virtual/cblas - virtual/lapack - sci-libs/clapack - sci-libs/arpack - sci-chemistry/mopac7 - sci-libs/netcdf - sci-libs/netcdf-fortran - >=sci-libs/fftw-3.3:3.0 - sci-chemistry/reduce" -DEPEND="${RDEPEND} - app-shells/tcsh - dev-util/byacc - dev-libs/libf2c - sys-devel/ucpp" - -S="${WORKDIR}/amber14" - -pkg_nofetch() { - einfo "Go to ${HOMEPAGE} and get AmberTools${PV%_p*}.tar.bz2" - einfo "Place it into ${DISTDIR}" -} - -pkg_setup() { - fortran-2_pkg_setup - export AMBERHOME="${S}" -} - -src_prepare() { - eapply \ - "${FILESDIR}"/${PN}-15-gentoo.patch - eapply -p0 \ - "${FILESDIR}"/${PN}-15-update.{1..6}.patch - - eapply_user - - cd "${S}"/AmberTools/src || die - rm -r \ - arpack \ - blas \ - byacc \ - lapack \ - fftw-3.3 \ - c9x-complex \ - netcdf-fortran-4.2 \ - netcdf-4.3.0 \ - reduce \ - ucpp-1.3 \ - || die - - cd "${S}"/AmberTools/src || die - sed \ - -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \ - -e "s:\\\\\$(LIBDIR)/lapack.a:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \ - -e "s:-llapack:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \ - -e "s:\\\\\$(LIBDIR)/blas.a:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \ - -e "s:-lblas:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \ - -e "s:GENTOO_CFLAGS:${CFLAGS}:g" \ - -e "s:GENTOO_CXXFLAGS:${CXXFLAGS}:g" \ - -e "s:GENTOO_FFLAGS:${FFLAGS}:g" \ - -e "s:GENTOO_LDFLAGS:${LDFLAGS}:g" \ - -e "s:GENTOO_INCLUDE:${EPREFIX}/usr/include:g" \ - -e "s:GENTOO_FFTW3_LIBS:$($(tc-getPKG_CONFIG) fftw3 --libs):" \ - -e "s:fc=g77:fc=$(tc-getFC):g" \ - -e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \ - -e "s:\$netcdf_flag:$($(tc-getPKG_CONFIG) netcdf --libs):g" \ - -e "s:\$netcdfflagc:$($(tc-getPKG_CONFIG) netcdf --libs):g" \ - -e "s:\$netcdfflagf:$($(tc-getPKG_CONFIG) netcdf-fortran --libs):g" \ - -i configure2 || die - - sed \ - -e "s:arsecond_:arscnd_:g" \ - -i sff/time.c sff/sff.h sff/sff.c || die - -} - -src_configure() { - python_setup - - local myconf="--no-updates" - - use X || myconf="${myconf} -noX11" - - cd "${S}" || die - - sed \ - -e '/patch_amber.py/d' \ - -i configure || die - - ./configure \ - ${myconf} \ - -nomtkpp \ - --with-python ${PYTHON} \ - --with-netcdf /usr \ - gnu || die -} - -src_compile() { - emake \ - CC=$(tc-getCC) \ - FC=$(tc-getFC) -} - -src_test() { - source ${AMBERHOME}/amber.sh - - emake test -} - -src_install() { - local x - 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" || die - for x in * - do - dosym ../../../bin/${x} /usr/share/${PN}/bin/${x} - done - cd "${S}" || die - - dodoc doc/Amber15.pdf - - dolib.a lib/*.a - dolib.so lib/*.so - - local m=( - chemistry - compat24.py - cpinutils - fortranformat - interface - mcpb - mdoutanalyzer - MMPBSA_mods - ParmedTools - pymsmtexp.py - pymsmtlib - pymsmtmol - sander - sanderles - ) - for x in ${m[@]} - do - python_domodule lib/${EPYTHON}/site-packages/${x} - done - - insinto /usr/include/${PN} - doins include/* - - insinto /usr/share/${PN} - doins -r dat - cd AmberTools || die - doins -r benchmarks examples test - - cat >> "${T}"/99ambertools <<- EOF - AMBERHOME="${EPREFIX}/usr/share/ambertools" - EOF - doenvd "${T}"/99ambertools -} diff --git a/sci-chemistry/ambertools/files/ambertools-12-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-12-gentoo.patch deleted file mode 100644 index 110343e22..000000000 --- a/sci-chemistry/ambertools/files/ambertools-12-gentoo.patch +++ /dev/null @@ -1,1345 +0,0 @@ - AmberTools/src/Makefile | 42 +- - AmberTools/src/configure2 | 63 +- - AmberTools/src/cpptraj/src/Makefile_at | 14 +- - AmberTools/src/mdgx/Makefile | 9 +- - AmberTools/src/mdgx/Trajectory.c | 2 +- - .../src/mmpbsa_py/MMPBSA_mods/amber_outputs.py | 4 +- - AmberTools/src/nab/database.c | 2 +- - AmberTools/src/nab/nab.c | 4 +- - AmberTools/src/pbsa/Makefile | 44 +- - AmberTools/src/ptraj/Makefile | 9 +- - AmberTools/src/ptraj/trajectory.c | 2 +- - AmberTools/src/sff/Makefile | 4 +- - AmberTools/src/sff/dsarpack.f | 654 +++++++++++++++++++++ - AmberTools/src/sqm/Makefile | 7 +- - AmberTools/test/Makefile | 4 +- - .../01_Generalized_Born/energies.csv.save | 8 +- - AmberTools/test/nab/Makefile | 2 + - AmberTools/test/nab/Run.rism_sp | 2 +- - AmberTools/test/nab/Run.rism_sp2 | 2 +- - AmberTools/test/test_at_serial.sh | 6 + - Makefile | 2 +- - 21 files changed, 725 insertions(+), 161 deletions(-) - -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..13efc78 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) - - -@@ -63,7 +63,7 @@ xminC.o: sff.h - AmberNetcdf.o: AmberNetcdf.h - - hcp_getpdb: hcp_getpdb.c -- $(CC) -o $(BINDIR)/hcp_getpdb hcp_getpdb.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(BINDIR)/hcp_getpdb hcp_getpdb.c - - .PHONY: ../rism/amber_rism_interface.NAB.o - ../rism/amber_rism_interface.NAB.o: -diff --git a/AmberTools/src/sff/dsarpack.f b/AmberTools/src/sff/dsarpack.f -new file mode 100644 -index 0000000..5544df9 ---- /dev/null -+++ 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/Makefile b/AmberTools/test/Makefile -index 27afe24..4796250 100644 ---- a/AmberTools/test/Makefile -+++ b/AmberTools/test/Makefile -@@ -3,14 +3,14 @@ include ../src/config.h - ###### Top-level targets, for general use: ############################ - - test: -- ./test_at_serial.sh -+ +./test_at_serial.sh - - test.parallel: - ./test_at_parallel.sh - - ###### Intermediate-level targets: ############################ - --test.serial: clean is_amberhome_defined \ -+test.serial: is_amberhome_defined \ - test.nab test.ptraj test.cpptraj test.antechamber \ - test.leap test.resp test.pbsa test.mmpbsa test.parmed \ - test.ambpdb test.elsize test.chamber test.sqm test.rism1d \ -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/Makefile b/AmberTools/test/nab/Makefile -index 1bb2505..7459a15 100644 ---- a/AmberTools/test/nab/Makefile -+++ b/AmberTools/test/nab/Makefile -@@ -12,6 +12,8 @@ testrism: \ - rism_ion-noasymp rism_ion_pse1 rism_ion_pse3 rism_mdiis0 rism_mdiis1 \ - rism_sp rism_sp2 - -+.NOTPARALLEL: -+ - duplex_test:: - @./Run.duplex - -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 -diff --git a/AmberTools/test/test_at_serial.sh b/AmberTools/test/test_at_serial.sh -index 15bb590..8fa52e3 100755 ---- a/AmberTools/test/test_at_serial.sh -+++ b/AmberTools/test/test_at_serial.sh -@@ -39,3 +39,9 @@ fi - - # save summary for later reporting: - tail -5 ${logfile} > ${logdir}/at_summary -+ -+if [ "${questionable_count}" -ne 0 -o "${error_count}" -ne 0 ] -+then -+ # Tests failed -+ exit 1 -+fi -diff --git a/Makefile b/Makefile -index 54ddfcb..643ba15 100644 ---- a/Makefile -+++ b/Makefile -@@ -30,7 +30,7 @@ clean.test: - test:: test.$(INSTALLTYPE) - - test.serial: -- -(cd AmberTools/test && $(MAKE) test) -+ (cd AmberTools/test && $(MAKE) test) - -@(if [ -n "$(BUILDAMBER)" ] ; then \ - cd test && $(MAKE) test; \ - echo "" ; \ diff --git a/sci-chemistry/ambertools/files/ambertools-12_p38-format-security.patch b/sci-chemistry/ambertools/files/ambertools-12_p38-format-security.patch deleted file mode 100644 index bb22a627a..000000000 --- a/sci-chemistry/ambertools/files/ambertools-12_p38-format-security.patch +++ /dev/null @@ -1,100 +0,0 @@ - AmberTools/src/mdgx/ChargeFit.c | 4 ++-- - AmberTools/src/nab/cgen.c | 2 +- - AmberTools/src/nab/traceback.c | 2 +- - AmberTools/src/ptraj/cluster.c | 2 +- - AmberTools/src/ptraj/interface.c | 6 +++--- - AmberTools/src/semantics/parse.c | 2 +- - 6 files changed, 9 insertions(+), 9 deletions(-) - -diff --git a/AmberTools/src/mdgx/ChargeFit.c b/AmberTools/src/mdgx/ChargeFit.c -index fccf5d0..fe4afac 100644 ---- a/AmberTools/src/mdgx/ChargeFit.c -+++ b/AmberTools/src/mdgx/ChargeFit.c -@@ -77,9 +77,9 @@ static void AssignGridTopologies(fset *myfit, prmtop *tp) - } - for (i = 0; i < myfit->ngrd; i++) { - if (myfit->tpname.map[i][0] == '\0') { -- sprintf(myfit->tpname.map[i], tp->source); -+ sprintf(myfit->tpname.map[i], "%s", tp->source); - if (myfit->eprule.map[i][0] == '\0' && tp->eprulesource[0] != '\0') { -- sprintf(myfit->eprule.map[i], tp->eprulesource); -+ sprintf(myfit->eprule.map[i], "%s", tp->eprulesource); - } - } - } -diff --git a/AmberTools/src/nab/cgen.c b/AmberTools/src/nab/cgen.c -index 6254d44..e206879 100644 ---- a/AmberTools/src/nab/cgen.c -+++ b/AmberTools/src/nab/cgen.c -@@ -1642,7 +1642,7 @@ static char *CG_gentype( char *csp, NODE_T *npt ) - strcpy( csp, tname ); - csp += strlen( csp ); - }else -- fprintf( cg_cfp, tname ); -+ fprintf( cg_cfp, "%s", tname ); - needspace = TRUE; - return( csp ); - } -diff --git a/AmberTools/src/nab/traceback.c b/AmberTools/src/nab/traceback.c -index f916474..e376552 100644 ---- a/AmberTools/src/nab/traceback.c -+++ b/AmberTools/src/nab/traceback.c -@@ -6,7 +6,7 @@ - int rt_errormsg( int fatal, char msg[] ) - { - -- fprintf( stderr, msg ); -+ fprintf( stderr, "%s", msg ); - if( fatal ) - exit( 1 ); - return(0); -diff --git a/AmberTools/src/ptraj/cluster.c b/AmberTools/src/ptraj/cluster.c -index 2cb60f0..5e0f33d 100644 ---- a/AmberTools/src/ptraj/cluster.c -+++ b/AmberTools/src/ptraj/cluster.c -@@ -1240,7 +1240,7 @@ void ClusteringMergeNames(PtrajClustering* This, ClusterNode* MergeNodeA, Cluste - { - return; - } -- sprintf(Temp, ClusterB->Name); -+ sprintf(Temp, "%s", ClusterB->Name); - sprintf(ClusterB->Name, "(%s,%s)", ClusterA->Name, Temp); - - } -diff --git a/AmberTools/src/ptraj/interface.c b/AmberTools/src/ptraj/interface.c -index 4087fa7..1ee4273 100644 ---- a/AmberTools/src/ptraj/interface.c -+++ b/AmberTools/src/ptraj/interface.c -@@ -97,8 +97,8 @@ interface(interfaceMode mode, char *filename) - - tokenlist = (Token *) &rdparmTokenlist; - -- fprintf(stdout, rdparm_header); -- fprintf(stdout, rdparm_prompt); -+ fprintf(stdout, "%s", rdparm_header); -+ fprintf(stdout, "%s", rdparm_prompt); - while (1) { - - fflush(stdout); -@@ -112,7 +112,7 @@ interface(interfaceMode mode, char *filename) - - } - -- fprintf(stdout, rdparm_prompt); -+ fprintf(stdout, "%s", rdparm_prompt); - } - } - } -diff --git a/AmberTools/src/semantics/parse.c b/AmberTools/src/semantics/parse.c -index 55c724c..68f23da 100644 ---- a/AmberTools/src/semantics/parse.c -+++ b/AmberTools/src/semantics/parse.c -@@ -2039,7 +2039,7 @@ int n_tab; - DEF_T tab[]; - { - -- fprintf( fp, oval ); -+ fprintf( fp, "%s", oval ); - - } - diff --git a/sci-chemistry/ambertools/files/ambertools-12_p38-gcc5.patch b/sci-chemistry/ambertools/files/ambertools-12_p38-gcc5.patch deleted file mode 100644 index 92e64954f..000000000 --- a/sci-chemistry/ambertools/files/ambertools-12_p38-gcc5.patch +++ /dev/null @@ -1,28 +0,0 @@ - AmberTools/src/configure2 | 14 ++++++++------ - 1 file changed, 8 insertions(+), 6 deletions(-) - -diff --git a/AmberTools/src/configure2 b/AmberTools/src/configure2 -index 913c50d..1232f6a 100755 ---- a/AmberTools/src/configure2 -+++ b/AmberTools/src/configure2 -@@ -703,12 +703,14 @@ gnu) - # if gcc <= 4.2, fftw3 is not compiled and pbsa fft solver and rism - # are disabled - if [ "$rism" != 'no' -o -n "$pbsaflag" ]; then -- if ( [ $gnu_majorversion -ge 4 ] && [ $gnu_minorversion -le 2 ] ) \ -- || [ $gnu_majorversion -le 3 ]; then -- echo "ERROR: RISM and PBSA FFT solver require version 4.3 or higher of the GNU compiler." -- echo " Please re-run configure with the '-nofftw3' flag to use this compiler:" -- echo " `mod_command_args '-rism' '-nofftw3'`" -- exit 1 -+ if [ $gnu_majorversion -lt 5 ]; then -+ if ( [ $gnu_majorversion -ge 4 ] && [ $gnu_minorversion -le 2 ] ) \ -+ || [ $gnu_majorversion -le 3 ]; then -+ echo "ERROR: RISM and PBSA FFT solver require version 4.3 or higher of the GNU compiler." -+ echo " Please re-run configure with the '-nofftw3' flag to use this compiler:" -+ echo " `mod_command_args '-rism' '-nofftw3'`" -+ exit 1 -+ fi - fi - fi - diff --git a/sci-chemistry/ambertools/files/ambertools-15-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-15-gentoo.patch deleted file mode 100644 index 76be4f8af..000000000 --- a/sci-chemistry/ambertools/files/ambertools-15-gentoo.patch +++ /dev/null @@ -1,1428 +0,0 @@ -diff --git a/AmberTools/src/Makefile b/AmberTools/src/Makefile -index 3d69773..71c794c 100644 ---- a/AmberTools/src/Makefile -+++ b/AmberTools/src/Makefile -@@ -15,12 +15,6 @@ 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 pbsa && $(MAKE) install ) - (cd gbnsr6 && $(MAKE) install ) - (cd cifparse && $(MAKE) install ) -@@ -33,7 +27,6 @@ serial: configured_serial THIRDPARTY $(MTKPP) - $(MAKE) cpptraj - - # miscellaneous: -- (cd reduce && $(MAKE) install ) - - # leap - (cd leap && $(MAKE) install ) -@@ -103,12 +96,6 @@ serial: configured_serial THIRDPARTY $(MTKPP) - - nabonly: configured_serial $(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 ) -@@ -144,12 +131,7 @@ parallel: configured_parallel THIRDPARTY - # (cd pbsa && $(MAKE) clean && $(MAKE) install.parallel ) - (cd pbsa && $(MAKE) libinstall ) - $(MAKE) cpptraj -- (cd byacc && $(MAKE) install ) -- (cd ucpp-1.3 && $(MAKE) $(UCPP) ) - (cd cifparse && $(MAKE) install ) -- (cd arpack && $(MAKE) install ); -- (cd lapack && $(MAKE) $(LAPACK) ) -- (cd blas && $(MAKE) $(BLAS) ) - (cd mdgx && $(MAKE) $(MDGX) ) - (if [ "$(RISM)" = "yes" ]; then \ - cd rism && $(MAKE) install_mpi ; \ -@@ -215,18 +197,12 @@ netcdf_uninstall: - -/bin/rm -f netcdf_config.log ../lib/libnetcdf* ../include/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 ) -@@ -236,15 +212,12 @@ 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 saxs && $(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 && /bin/rm -fr MMPBSA.py.MPI build/ mpi4py-1.2.2/) - -(cd mm_pbsa && $(MAKE) clean ) - -(cd FEW && $(MAKE) clean ) -@@ -315,7 +288,7 @@ $(LIBDIR)/libxblas-amb.a: - $(LIBDIR)/libfftw3.a $(LIBDIR)/libfftw3_mpi.a: - cd fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install; - --THIRDPARTY: $(XBLAS) $(FFTW3) -+THIRDPARTY: $(XBLAS) - - cuda: - @echo "$(AMBERTOOLS) has no CUDA-enabled components" -diff --git a/AmberTools/src/configure2 b/AmberTools/src/configure2 -index f1a3cff..4b07fa5 100755 ---- a/AmberTools/src/configure2 -+++ b/AmberTools/src/configure2 -@@ -318,7 +318,7 @@ fi - #------------------------------------------------------------------------------ - # Define variables that are currently constants: - #------------------------------------------------------------------------------ --bintraj='yes' -+bintraj='no' - ldout=' -o ' - localcp='cp' - localmv='mv' -@@ -358,7 +358,7 @@ cygwin='no' - debug='no' - dragonegg='' - fpp="cpp -traditional -P" --fppflags='' -+fppflags='-DBINTRAJ' - freeformat_flag='' - fwarnflag='' - g95='no' -@@ -370,7 +370,7 @@ installtype='serial' - intel_compiler_flag_mkl='no' - intelmpi='no' - is_mac='no' --ldflags='' -+ldflags='GENTOO_LDFLAGS' - ld='ld ' - lfs='yes' - lm='-lm' -@@ -599,11 +599,11 @@ 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? -@@ -907,7 +907,7 @@ gnu) - flibs_arch="-lgfortran -w" - flibsf_arch= - cc=gcc -- cflags="-fPIC" -+ cflags="-fPIC -DBINTRAJ" - ambercflags="" - cplusplus=g++ - cxxflags="-fPIC" -@@ -937,11 +937,11 @@ gnu) - foptflags="" - else - cnooptflags= -- coptflags="-O3" -+ coptflags="GENTOO_CFLAGS" - cxxnooptflags= -- cxxoptflags="-fPIC -O3" -+ cxxoptflags="-fPIC GENTOO_CXXFLAGS" - fnooptflags="-O0" -- foptflags="-O3" -+ foptflags="GENTOO_FFLAGS" - fi - - # Debugging options -@@ -957,11 +957,11 @@ gnu) - if [ $sse = 'yes' ]; then - if [ $x86_64 = 'yes' ]; then - #-mfpmath=sse is default for x86_64, no need to specific it -- coptflags="$coptflags -mtune=native" -- foptflags="$foptflags -mtune=native" -+ coptflags="$coptflags" -+ foptflags="$foptflags" - else # i386 needs to be told to use sse prior to using -mfpmath=sse -- coptflags="$coptflags -mtune=native -msse -mfpmath=sse" -- foptflags="$foptflags -mtune=native -msse -mfpmath=sse" -+ coptflags="$coptflags" -+ foptflags="$foptflags" - fi - fi - fcreal8="-fdefault-real-8" -@@ -1032,7 +1032,7 @@ gnu) - # pmemd_fpp_flags='-DFFTW_FFT' - # fi - pmemd_foptflags="$foptflags" -- pmemd_coptflags="$coptflags" -+ pmemd_coptflags="$coptflags -DBINTRAJ" - if [ ! -z $dragonegg ]; then - pmemd_foptflags="-fplugin=$dragonegg $fflags $pmemd_foptflags" - pmemd_coptflags="-fplugin=$dragonegg $pmemd_coptflags" -@@ -1062,7 +1062,7 @@ gnu) - fi - pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" - pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" -- pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK" -+ pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK -DBINTRAJ" - fi - fi - if [ "$cuda_SPFP" = 'yes' ]; then -@@ -2649,40 +2649,40 @@ if [ "$has_fftw3" = 'yes' ]; then - if [ "$sse" = "yes" ]; then - enable_sse="--enable-sse2=yes" # --enable-avx=yes" - fi -- if [ "$mic" = 'yes' ]; then -- echo " --configuring for mic (native mode)..." -- echo -- cd fftw-3.3 && \ -- ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \ -- --enable-static --enable-shared --host=x86_64-k1om-linux \ -- --build=x86_64-unknown-linux \ -- $enable_mpi $mpicc $enable_debug \ -- CC="$cc -mmic" CFLAGS="$cflags $coptflags " \ -- F77="$fc -mmic" FFLAGS="$fflags $foptflags " \ -- FLIBS="$flibs_arch" \ -- > ../fftw3_config.log 2>&1 -- ncerror=$? -- else -- cd fftw-3.3 && \ -- ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \ -- --enable-static --enable-shared \ -- $enable_mpi $mpicc $enable_debug $enable_sse\ -- CC="$cc" CFLAGS="$cflags $coptflags" \ -- F77="$fc" FFLAGS="$fflags $foptflags" \ -- FLIBS="$flibs_arch" \ -- > ../fftw3_config.log 2>&1 -- ncerror=$? -- fi -- if [ $ncerror -gt 0 ]; then -- echo "Error: FFTW configure returned $ncerror" -- echo " FFTW configure failed! Check the fftw3_config.log file" -- echo " in the $AMBERHOME/AmberTools/src directory." -- exit 1 -- else -- echo " fftw-3.3 configure succeeded." -- fi -- cd .. -- flibs_fftw3="-lfftw3" -+# if [ "$mic" = 'yes' ]; then -+# echo " --configuring for mic (native mode)..." -+# echo -+# cd fftw-3.3 && \ -+# ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \ -+# --enable-static --enable-shared --host=x86_64-k1om-linux \ -+# --build=x86_64-unknown-linux \ -+# $enable_mpi $mpicc $enable_debug \ -+# CC="$cc -mmic" CFLAGS="$cflags $coptflags " \ -+# F77="$fc -mmic" FFLAGS="$fflags $foptflags " \ -+# FLIBS="$flibs_arch" \ -+# > ../fftw3_config.log 2>&1 -+# ncerror=$? -+# else -+# cd fftw-3.3 && \ -+# ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \ -+# --enable-static --enable-shared \ -+# $enable_mpi $mpicc $enable_debug $enable_sse\ -+# CC="$cc" CFLAGS="$cflags $coptflags" \ -+# F77="$fc" FFLAGS="$fflags $foptflags" \ -+# FLIBS="$flibs_arch" \ -+# > ../fftw3_config.log 2>&1 -+# ncerror=$? -+# fi -+# if [ $ncerror -gt 0 ]; then -+# echo "Error: FFTW configure returned $ncerror" -+# echo " FFTW configure failed! Check the fftw3_config.log file" -+# echo " in the $AMBERHOME/AmberTools/src directory." -+# exit 1 -+# else -+# echo " fftw-3.3 configure succeeded." -+# fi -+# cd .. -+ flibs_fftw3="GENTOO_FFTW3_LIBS" - fftw3="\$(LIBDIR)/libfftw3.a" - if [ "$mpi" = 'yes' -a "$intelmpi" = 'no' ]; then - flibs_fftw3="-lfftw3_mpi $flibs_fftw3" -@@ -2701,23 +2701,23 @@ elif [ "$mdgx" = 'yes' ]; then - 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 --enable-shared --disable-fortran \ -- $enable_debug $enable_sse\ -- CC="$cc" CFLAGS="$cflags $coptflags" \ -- > ../fftw3_config.log 2>&1 -- ncerror=$? -- if [ $ncerror -gt 0 ]; then -- echo "Error: FFTW configure returned $ncerror" -- echo " FFTW configure failed! Check the fftw3_config.log file" -- echo " in the $AMBERHOME/AmberTools/src directory." -- exit 1 -- else -- echo " fftw-3.3 configure succeeded." -- fi -- cd .. -- flibs_fftw3="-lfftw3" -+# cd fftw-3.3 && \ -+# ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \ -+# --enable-static --enable-shared --disable-fortran \ -+# $enable_debug $enable_sse\ -+# CC="$cc" CFLAGS="$cflags $coptflags" \ -+# > ../fftw3_config.log 2>&1 -+# ncerror=$? -+# if [ $ncerror -gt 0 ]; then -+# echo "Error: FFTW configure returned $ncerror" -+# echo " FFTW configure failed! Check the fftw3_config.log file" -+# echo " in the $AMBERHOME/AmberTools/src directory." -+# exit 1 -+# else -+# echo " fftw-3.3 configure succeeded." -+# fi -+# cd .. -+ flibs_fftw3="GENTOO_FFTW3_LIBS" - fftw3="\$(LIBDIR)/libfftw3.a" - else - echo "" -@@ -3162,7 +3162,7 @@ LDFLAGS=$ldflags \$(CUSTOMBUILDFLAGS) \$(AMBERBUILDFLAGS) - AMBERLDFLAGS=\$(AMBERBUILDFLAGS) - - LEX= $lex --YACC= \$(BINDIR)/yacc -+YACC= byacc - AR= ar rv - M4= $m4 - RANLIB=$ranlib -@@ -3198,7 +3198,7 @@ CP=$localcp - # Information about Fortran compilation: - - FC=$fc --FFLAGS= $fflags \$(LOCALFLAGS) \$(CUSTOMBUILDFLAGS) -I\$(INCDIR) \$(NETCDFINC) $mklinc \$(AMBERBUILDFLAGS) -+FFLAGS= $fflags \$(LOCALFLAGS) \$(CUSTOMBUILDFLAGS) -IGENTOO_INCLUDE \$(NETCDFINC) $mklinc \$(AMBERBUILDFLAGS) - FNOOPTFLAGS= $fnooptflags - FOPTFLAGS= $foptflags - AMBERFFLAGS=\$(AMBERBUILDFLAGS) -diff --git a/AmberTools/src/cpptraj/src/Makefile_at b/AmberTools/src/cpptraj/src/Makefile_at -index 977439f..4bf25c8 100644 ---- a/AmberTools/src/cpptraj/src/Makefile_at -+++ b/AmberTools/src/cpptraj/src/Makefile_at -@@ -10,7 +10,7 @@ CPPTRAJ_FLAGS= -I$(INCDIR) $(COPTFLAGS) $(CFLAGS) $(NETCDFINC) - # NOTE: Since -nobintraj is possible and the dependency for netcdf is not - # set correctly by configure there is no way this can work for netcdf - READLINE_HOME=readline --READLINE=$(READLINE_HOME)/libreadline.a -+READLINE=-lreadline - EXTERNAL_LIBS=$(LIBDIR)/libarpack.a $(LIBDIR)/liblapack.a $(LIBDIR)/libblas.a $(READLINE) - - include cpptrajfiles -@@ -45,7 +45,7 @@ depend: findDepend - dependclean: - /bin/rm -f FindDepend.o findDepend - --cpptraj$(SFX): $(OBJECTS) pub_fft.o $(EXTERNAL_LIBS) -+cpptraj$(SFX): $(OBJECTS) pub_fft.o - $(CXX) $(WARNFLAGS) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) pub_fft.o \ - -L$(LIBDIR) $(NETCDFLIB) $(ZLIB) $(BZLIB) $(FLIBS_PTRAJ) $(READLINE) - -@@ -53,12 +53,12 @@ ambpdb$(SFX): $(AMBPDB_OBJECTS) - $(CXX) $(WARNFLAGS) $(LDFLAGS) -o ambpdb$(SFX) $(AMBPDB_OBJECTS) \ - -L$(LIBDIR) $(NETCDFLIB) $(ZLIB) $(BZLIB) - --cpptraj.sander$(SFX): $(OBJECTS) pub_fft.o $(EXTERNAL_LIBS) $(LIBDIR)/libsander.so -+cpptraj.sander$(SFX): $(OBJECTS) pub_fft.o $(LIBDIR)/libsander.so - $(CXX) $(WARNFLAGS) $(LDFLAGS) -o cpptraj.sander$(SFX) $(OBJECTS) pub_fft.o \ - -L$(LIBDIR) $(NETCDFLIB) $(ZLIB) $(BZLIB) $(FLIBS_PTRAJ) $(READLINE) \ - -lsander - --libcpptraj$(SHARED_SUFFIX): $(OBJECTS) pub_fft.o $(EXTERNAL_LIBS) -+libcpptraj$(SHARED_SUFFIX): $(OBJECTS) pub_fft.o - $(CXX) $(MAKE_SHARED) $(WARNFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) pub_fft.o \ - -L$(LIBDIR) $(NETCDFLIB) $(ZLIB) $(BZLIB) $(FLIBS_PTRAJ) $(READLINE) - -diff --git a/AmberTools/src/gbnsr6/Makefile b/AmberTools/src/gbnsr6/Makefile -index 0d704cb..85042d4 100644 ---- a/AmberTools/src/gbnsr6/Makefile -+++ b/AmberTools/src/gbnsr6/Makefile -@@ -66,7 +66,7 @@ configured_serial: configured - ) - - #--------------------------------------------------------------------------- --gbnsr6$(SFX): $(OBJ) syslib netlib c9x-complex configured_serial -+gbnsr6$(SFX): $(OBJ) syslib configured_serial - $(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o gbnsr6$(SFX) $(OBJ) \ - ../lib/nxtsec.o ../lib/random.o \ - -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS) -diff --git a/AmberTools/src/mdgx/Makefile b/AmberTools/src/mdgx/Makefile -index 5751142..04e8e1c 100644 ---- a/AmberTools/src/mdgx/Makefile -+++ b/AmberTools/src/mdgx/Makefile -@@ -151,7 +151,7 @@ MDGX_HEADERS = \ - ptrajmask.h \ - AmberNetcdf.h - --$(BINDIR)/mdgx$(SFX) : $(FFTW3) $(MDGX_OBJS) -+$(BINDIR)/mdgx$(SFX) : $(MDGX_OBJS) - $(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) \ - -o $@ $(MDGX_OBJS) -L$(LIBDIR) $(FLIBS_FFTW3) $(NETCDFLIB) $(LM) - -@@ -159,7 +159,7 @@ $(BINDIR)/mdgx.MPI$(SFX) : $(MDGX_OBJS) - $(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) \ - -o $@ $(MDGX_OBJS) -L$(LIBDIR) $(FLIBSF) $(FLIBS_FFTW3) $(NETCDFLIB) $(LM) - --$(LIBDIR)/libmdgx$(SHARED_SUFFIX): $(MDGX_OBJS) $(MDGXWRAP_OBJS) $(BINDIR)/ucpp -+$(LIBDIR)/libmdgx$(SHARED_SUFFIX): $(MDGX_OBJS) $(MDGXWRAP_OBJS) - $(CC) $(MAKE_SHARED) -o $@ $(CFLAGS) $(COPTFLAGS) -L$(LIBDIR) $(FLIBSF) \ - $(FLIBS_FFTW3) $(NETCDFLIB) $(LM) $(MDGX_OBJS) $(MDGXWRAP_OBJS) - cp -p mdgxapi.h $(INCDIR)/mdgx.h -diff --git a/AmberTools/src/nab/nab.c b/AmberTools/src/nab/nab.c -index 2e90068..cf83aaa 100644 ---- a/AmberTools/src/nab/nab.c -+++ b/AmberTools/src/nab/nab.c -@@ -161,8 +161,8 @@ char *cppstring; - fprintf( stderr, "AMBERHOME is not set!\n" ); - exit(1); - } -- sprintf( cmd, "%s/bin/%s %s -I%s/include %s ", -- amberhome, CPP, cppstring, amberhome, -+ sprintf( cmd, "%s %s -I%s/include %s ", -+ CPP, cppstring, amberhome, - argv[ ac ] ? argv[ ac ] : "" ); - if( cgdopt ) fprintf( stderr, "cpp cmd: %s\n", cmd ); - nfields = split( cmd, fields, " " ); -diff --git a/AmberTools/src/nmode/Makefile b/AmberTools/src/nmode/Makefile -index 12acf35..4f26593 100644 ---- a/AmberTools/src/nmode/Makefile -+++ b/AmberTools/src/nmode/Makefile -@@ -87,12 +87,12 @@ LIBOBJ= ../lib/rfree.o ../lib/matinv.o ../lib/nxtsec.o \ - LIBOBJNOPATH= rfree.o matinv.o nxtsec.o \ - amopen.o rgroup.o - --$(BINDIR)/nmode$(SFX): $(OBJ) libobj syslib netlib -+$(BINDIR)/nmode$(SFX): $(OBJ) libobj syslib - $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $(BINDIR)/nmode$(SFX) \ - $(OBJ) $(LIBOBJ) \ - ../lib/sys.a -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS) - --nmanal$(SFX): $(OBJ1) libobj netlib binpos.o -+nmanal$(SFX): $(OBJ1) libobj binpos.o - $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o nmanal$(SFX) \ - $(OBJ1) $(LIBOBJ) binpos.o \ - -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS) -@@ -103,7 +103,7 @@ lmanal$(SFX): $(OBJ2) libobj binpos.o - -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS) - - quasih$(SFX): quasih.o fileio.o thermo.o mexit.o \ -- syslib netlib libobj binpos.o -+ syslib libobj binpos.o - $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o quasih$(SFX) \ - quasih.o fileio.o thermo.o mexit.o \ - $(LIBOBJ) binpos.o ../lib/sys.a -L$(LIBDIR) $(FLIBSF) \ -diff --git a/AmberTools/src/pbsa/Makefile b/AmberTools/src/pbsa/Makefile -index 1b2c09a..6dc65a6 100644 ---- a/AmberTools/src/pbsa/Makefile -+++ b/AmberTools/src/pbsa/Makefile -@@ -148,23 +148,23 @@ configured_parallel: configured - ) - - #--------------------------------------------------------------------------- --pbsa$(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 - $(RANLIB) libpbsa.a -diff --git a/AmberTools/src/ptraj/Makefile b/AmberTools/src/ptraj/Makefile -index df789e8..48227d5 100644 ---- a/AmberTools/src/ptraj/Makefile -+++ b/AmberTools/src/ptraj/Makefile -@@ -61,17 +61,16 @@ rdparm$(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) -diff --git a/AmberTools/src/sander/Makefile b/AmberTools/src/sander/Makefile -index 9b9488c..de25fc7 100644 ---- a/AmberTools/src/sander/Makefile -+++ b/AmberTools/src/sander/Makefile -@@ -90,7 +90,7 @@ APBSOBJ= \ - file_io_dat.APBS.o apbs_vars.APBS.o apbs.APBS.o \ - constants.o state.o memory_module.o stack.o \ - nose_hoover.o nose_hoover_init.o \ -- trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o \ -+ trace.o rmsgrd.o lmod.o rand2.o dsarpack.o lmodC.o xminC.o decomp.o \ - icosasurf.o egb.o remd.o findmask.o \ - relax_mat.o nmr.o multitmd.o \ - multisander.o sander.APBS.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o \ -@@ -138,7 +138,7 @@ SEBOMDLIB = ../sebomd/sebomd.a - - MMOBJ= file_io_dat.o constants.o state.o memory_module.o stack.o \ - nose_hoover.o nose_hoover_init.o \ -- trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o \ -+ trace.o rmsgrd.o lmod.o rand2.o dsarpack.o lmodC.o xminC.o decomp.o \ - icosasurf.o egb.o remd.o findmask.o \ - relax_mat.o nmr.o multitmd.o \ - multisander.o sander.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o \ -@@ -159,7 +159,7 @@ MMOBJ= file_io_dat.o constants.o state.o memory_module.o stack.o \ - - APIOBJ= file_io_dat.o constants.o state.o memory_module.o stack.o \ - nose_hoover.o nose_hoover_init.o \ -- trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o \ -+ trace.o rmsgrd.o lmod.o rand2.o dsarpack.o lmodC.o xminC.o decomp.o \ - icosasurf.o egb.o remd.o findmask.o \ - relax_mat.o nmr.o multitmd.o \ - trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o \ -@@ -180,7 +180,7 @@ APIOBJ= file_io_dat.o constants.o state.o memory_module.o stack.o \ - - LESAPIOBJ= memory_module.o stack.o file_io_dat.o les.o \ - constants.o state.o nose_hoover.o nose_hoover_init_LES.o \ -- trace.o rmsgrd.o rand2.o lmodC.o xminC.o decomp.o icosasurf.o \ -+ trace.o rmsgrd.o rand2.o dsarpack.o lmodC.o xminC.o decomp.o icosasurf.o \ - egb.LES.o remd.LES.o findmask.o relax_mat.o nmr.LES.o multitmd.o \ - cshf.o nmrcal.o mtmdcall.o pearsn.o cpparm.LES.o \ - printe.o runmin.o nonbond_list.LESAPI.o force.LES.o rdparm.LESAPI.o \ -@@ -209,7 +209,7 @@ PARTPIMDOBJ = pimd_vars.o pimd_force.LES.o pimd_init.LES.o cmd_vars.o cmd_matrix - - PUPILOBJ= file_io_dat.o constants.o state.o memory_module.o stack.o \ - nose_hoover.o nose_hoover_init.o \ -- trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o \ -+ trace.o rmsgrd.o lmod.o rand2.o dsarpack.o lmodC.o xminC.o decomp.o \ - pupildata.o icosasurf.o egb.o findmask.o \ - relax_mat.o nmr.o multitmd.o \ - multisander.o sander.PUPIL.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o \ -@@ -233,7 +233,7 @@ LSCIVROBJ = lscivr_vars.o lsc_init.o lsc_xp.o - - LESOBJ= memory_module.o stack.o file_io_dat.o \ - constants.o state.o nose_hoover.o nose_hoover_init_LES.o \ -- trace.o rmsgrd.o rand2.o lmodC.o xminC.o decomp.o icosasurf.o \ -+ trace.o rmsgrd.o rand2.o dsarpack.o lmodC.o xminC.o decomp.o icosasurf.o \ - egb.LES.o remd.LES.o findmask.o \ - relax_mat.o nmr.LES.o multitmd.o \ - multisander.LES.o sander.LES.o cshf.o nmrcal.o mtmdcall.o pearsn.o \ -@@ -293,7 +293,7 @@ all_serial_programs: $(SERIALPROGS) - $(BINDIR)/sander$(SFX): libsqm $(MMOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \ - $(SEBOMDOBJ) sebomd \ - $(LSCIVROBJ) force.o syslib \ -- ../lib/nxtsec.o netlib configured_serial \ -+ ../lib/nxtsec.o configured_serial \ - $(NCSU_OBJECTS) $(XRAY_OBJS) libpbsa librism $(PLUMED_DEPENDENCIES) - $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(MMOBJ) $(QMOBJ) $(SEBOMDOBJ) \ - $(FULLPIMDOBJ) $(LSCIVROBJ) force.o -L$(LIBDIR) -lsqm \ -@@ -308,7 +308,7 @@ $(BINDIR)/sander$(SFX): libsqm $(MMOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \ - $(BINDIR)/sander.MPI$(SFX): libsqm $(MMOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \ - $(LSCIVROBJ) $(EVBOBJ) force.o \ - $(SEBOMDOBJ) sebomd $(XRAY_OBJS) \ -- syslib ../lib/nxtsec.o netlib libpbsa librism_mpi configured_parallel $(NCSU_OBJECTS) \ -+ syslib ../lib/nxtsec.o libpbsa librism_mpi configured_parallel $(NCSU_OBJECTS) \ - $(PLUMED_DEPENDENCIES) - $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(MMOBJ) $(QMOBJ) $(SEBOMDOBJ) \ - $(FULLPIMDOBJ) $(LSCIVROBJ) $(EVBOBJ) force.o \ -@@ -323,7 +323,7 @@ $(BINDIR)/sander.MPI$(SFX): libsqm $(MMOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \ - $(BINDIR)/sander.PUPIL$(SFX): libsqm $(PUPILOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \ - $(LSCIVROBJ) syslib $(XRAY_OBJS) \ - $(SEBOMDOBJ) sebomd \ -- ../lib/nxtsec.o netlib libpbsa librism configured_serial $(NCSU_OBJECTS) \ -+ ../lib/nxtsec.o libpbsa librism configured_serial $(NCSU_OBJECTS) \ - $(PLUMED_DEPENDENCIES) - $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(PUPILOBJ) $(QMOBJ) $(SEBOMDOBJ) $(FULLPIMDOBJ) \ - $(LSCIVROBJ) -L$(LIBDIR) -lsqm -lFpbsa \ -@@ -335,7 +335,7 @@ $(BINDIR)/sander.PUPIL$(SFX): libsqm $(PUPILOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) - - #--------------------------------------------------------------------------- - $(BINDIR)/sander.LES$(SFX): libsqm $(LESOBJ) $(PARTPIMDOBJ) syslib \ -- ../lib/nxtsec.o netlib \ -+ ../lib/nxtsec.o \ - $(LSCIVROBJ) $(NCSU_OBJECTS) $(XRAY_OBJS) configured_serial \ - libpbsa librism $(EMIL) sebomd $(PLUMED_DEPENDENCIES) - $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(LESOBJ) $(PARTPIMDOBJ) $(LSCIVROBJ) \ -@@ -348,7 +348,7 @@ $(BINDIR)/sander.LES$(SFX): libsqm $(LESOBJ) $(PARTPIMDOBJ) syslib \ - #--------------------------------------------------------------------------- - $(BINDIR)/sander.LES.MPI$(SFX): libsqm $(LESOBJ) $(EVBPIMD) \ - $(PARTPIMDOBJ) syslib ../lib/nxtsec.o \ -- netlib libpbsa librism_mpi $(EMIL) $(XRAY_OBJS) \ -+ libpbsa librism_mpi $(EMIL) $(XRAY_OBJS) \ - $(LSCIVROBJ) $(NCSU_OBJECTS) sebomd configured_parallel $(PLUMED_DEPENDENCIES) - $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(LESOBJ) $(EVBPIMD) \ - $(PARTPIMDOBJ) $(LSCIVROBJ) $(XRAY_OBJS) \ -@@ -363,7 +363,7 @@ $(BINDIR)/sander.APBS$(SFX): libsqm $(APBSOBJ) $(QMOBJ) \ - $(LSCIVROBJ) $(FULLPIMDOBJ) $(NCSU_OBJECTS) \ - force.APBS.o syslib librism $(EMIL) \ - $(SEBOMDOBJ) sebomd $(XRAY_OBJS) \ -- ../lib/nxtsec.o netlib configured_serial $(PLUMED_DEPENDENCIES) -+ ../lib/nxtsec.o configured_serial $(PLUMED_DEPENDENCIES) - $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(APBSOBJ) $(QMOBJ) $(SEBOMDOBJ) \ - $(FULLPIMDOBJ) $(LSCIVROBJ) force.APBS.o \ - -L$(APBS_LIBDIR) $(APBS_LIBS) \ -@@ -386,7 +386,7 @@ $(BINDIR)/ambmask$(SFX): ambmask.o findmask.o amopen.o parms.o \ - $(LIBDIR)/libsander$(SHARED_SUFFIX): libsqm $(APIOBJ) $(QMAPIOBJ) $(FULLPIMDOBJ) $(EMIL) \ - $(SEBOMDOBJ) sebomd $(INCDIR)/sander_api.mod \ - $(LSCIVROBJ) force.o syslib $(PLUMED_DEPENDENCIES) \ -- ../lib/nxtsec.o netlib configured_serial \ -+ ../lib/nxtsec.o configured_serial \ - $(NCSU_OBJECTS) $(XRAY_OBJS) libpbsa librism - $(FC) $(MAKE_SHARED) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(APIOBJ) \ - $(QMAPIOBJ) $(SEBOMDOBJ) $(FULLPIMDOBJ) $(LSCIVROBJ) force.o \ -@@ -399,7 +399,7 @@ $(LIBDIR)/libsander$(SHARED_SUFFIX): libsqm $(APIOBJ) $(QMAPIOBJ) $(FULLPIMDOBJ) - $(LIOLIBS) $(PLUMED_LOAD) - - $(LIBDIR)/libsanderles$(SHARED_SUFFIX): libsqm $(LESAPIOBJ) $(PARTPIMDOBJ) $(QMAPIOBJ) syslib \ -- ../lib/nxtsec.o netlib $(INCDIR)/sanderles_api.mod \ -+ ../lib/nxtsec.o $(INCDIR)/sanderles_api.mod \ - $(LSCIVROBJ) $(NCSU_OBJECTS) $(XRAY_OBJS) configured_serial \ - libpbsa librism $(EMIL) sebomd $(PLUMED_DEPENDENCIES) - $(FC) $(MAKE_SHARED) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) \ -@@ -452,6 +452,10 @@ rand2.o: ../sff/rand2.c - $(CC) -c $(CNOOPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \ - -o rand2.o ../sff/rand2.c - -+dsarpack.o: ../sff/dsarpack.f -+ $(FC) -c $(FPPFLAGS) $(CFLAGS) $(AMBERFFLAGS) \ -+ -o dsarpack.o ../sff/dsarpack.f -+ - lmodC.o: ../sff/lmodC.c - $(CC) -c -DSQM $(CNOOPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \ - -o lmodC.o ../sff/lmodC.c -diff --git a/AmberTools/src/sander/depend b/AmberTools/src/sander/depend -index 67cc33b..b8667d7 100644 ---- a/AmberTools/src/sander/depend -+++ b/AmberTools/src/sander/depend -@@ -5774,7 +5774,7 @@ yammpnb.o: \ - yammpnb.o: yammpnb.F90 - $(FC) $(FWARNFLAGS) $(FPPFLAGS) -c $(FOPTFLAGS) $(FFLAGS) $(AMBERFFLAGS) $(RISMSANDER) -o $@ yammpnb.F90 - --netcdf.o: $(NETCDF) -+netcdf.o: - test -e $@ || touch netcdf.o - - AmberNetcdf.o: ../lib/AmberNetcdf.F90 -diff --git a/AmberTools/src/sander/makedepend b/AmberTools/src/sander/makedepend -index 05c04c4..a18d979 100755 ---- a/AmberTools/src/sander/makedepend -+++ b/AmberTools/src/sander/makedepend -@@ -232,7 +232,7 @@ foreach $file ( <*.F90> ){ - } - - # special "compilation rule" for netcdf.o --printf "netcdf.o: \$(NETCDF)\n\ttest -e \$\@ || touch netcdf.o\n\n"; -+printf "netcdf.o:\n\ttest -e \$\@ || touch netcdf.o\n\n"; - - # special compilation rule for AmberNetcdf.o, random.o, and constants.o - printf "AmberNetcdf.o: ../lib/AmberNetcdf.F90\n"; -diff --git a/AmberTools/src/sander/sander.h b/AmberTools/src/sander/sander.h -index e4ca7e3..23cb216 100644 ---- a/AmberTools/src/sander/sander.h -+++ b/AmberTools/src/sander/sander.h -@@ -47,7 +47,7 @@ - // Workaround for strange behavior of clang compiler -- clang C doesn't seem to - // like the inline specifier on any of these functions, but clang++ handles it - // just fine. --#if defined(__cplusplus) || !defined(__clang__) -+#if defined(__cplusplus) - # define INLINE inline - #else - # define INLINE -diff --git a/AmberTools/src/sff/Makefile b/AmberTools/src/sff/Makefile -index 228625a..88d5531 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 atomic_number.o $(SFF_RISM_INTERFACE) - - -@@ -65,7 +65,7 @@ xminC.o: sff.h - AmberNetcdf.o: AmberNetcdf.h - - hcp_getpdb: hcp_getpdb.c -- $(CC) -o $(BINDIR)/hcp_getpdb hcp_getpdb.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(BINDIR)/hcp_getpdb hcp_getpdb.c - - .PHONY: ../rism/amber_rism_interface.NAB.o - ../rism/amber_rism_interface.NAB.o: -diff --git a/AmberTools/src/sff/dsarpack.f b/AmberTools/src/sff/dsarpack.f -new file mode 100644 -index 0000000..5544df9 ---- /dev/null -+++ 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 a0fa790..5983764 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) - -diff --git a/AmberTools/test/Makefile b/AmberTools/test/Makefile -index 8252d52..24b9272 100644 ---- a/AmberTools/test/Makefile -+++ b/AmberTools/test/Makefile -@@ -3,14 +3,14 @@ include ../src/config.h - ###### Top-level targets, for general use: ############################ - - test:: -- ./test_at_serial.sh -+ +./test_at_serial.sh - - test.parallel:: - ./test_at_parallel.sh - - ###### Intermediate-level targets: ############################ - --test.serial: clean is_amberhome_defined \ -+test.serial: is_amberhome_defined \ - test.nab test.cpptraj test.antechamber test.mdgx \ - test.leap test.resp test.pbsa test.gbnsr6 test.mmpbsa test.parmed \ - test.elsize test.sqm test.rism1d test.amberlite \ -diff --git a/AmberTools/test/test_at_serial.sh b/AmberTools/test/test_at_serial.sh -index a154c84..c092eb6 100755 ---- a/AmberTools/test/test_at_serial.sh -+++ b/AmberTools/test/test_at_serial.sh -@@ -44,3 +44,9 @@ fi - - # save summary for later reporting: - tail -5 ${logfile} > ${logdir}/at_summary -+ -+if [ "${questionable_count}" -ne 0 -o "${error_count}" -ne 0 ] -+then -+ # Tests failed -+ exit 1 -+fi -diff --git a/AmberTools/test/test_check.sh b/AmberTools/test/test_check.sh -index 108c446..62c0b88 100644 ---- a/AmberTools/test/test_check.sh -+++ b/AmberTools/test/test_check.sh -@@ -63,7 +63,7 @@ check_environment() { - # We are done here for Macs - test $is_mac = "yes" && return - -- python << EOF -+ python2 << EOF - import os - import sys - ambhome = os.getenv('AMBERHOME') diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.1.patch b/sci-chemistry/ambertools/files/ambertools-15-update.1.patch deleted file mode 100644 index 28d25e590..000000000 --- a/sci-chemistry/ambertools/files/ambertools-15-update.1.patch +++ /dev/null @@ -1,118 +0,0 @@ -*******> update.1 - -Author: Jason Swails - -Date: June 1, 2015 - -Programs: MMPBSA.py, ParmEd, cpptraj - -Description: This fixes a number of small issues: - 1) Fix Python 2.4 and Python 2.5 support for ParmEd and MMPBSA.py - 2) Fix the MMPBSA.py Python API - 3) Scale charges correctly for LIE action in cpptraj with non-unity - dielectric constant - --------------------------------------------------------------------------------- - - AmberTools/src/cpptraj/src/Action_LIE.cpp | 2 +- - AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py | 3 ++- - AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py | 1 + - AmberTools/src/parmed/chemistry/__init__.py | 6 +++++- - .../test/mmpbsa_py/07_Comprehensive/Run.comprehensive | 18 ++++++++++++++++++ - 5 files changed, 27 insertions(+), 3 deletions(-) - -diff --git AmberTools/src/cpptraj/src/Action_LIE.cpp AmberTools/src/cpptraj/src/Action_LIE.cpp -index 25825c1..716a04f 100644 ---- AmberTools/src/cpptraj/src/Action_LIE.cpp -+++ AmberTools/src/cpptraj/src/Action_LIE.cpp -@@ -132,7 +132,7 @@ int Action_LIE::SetupParms(Topology const& ParmIn) { - atom_charge_.reserve( ParmIn.Natom() ); - for (Topology::atom_iterator atom = ParmIn.begin(); - atom != ParmIn.end(); ++atom) -- atom_charge_.push_back( atom->Charge() * Constants::ELECTOAMBER / dielc_ ); -+ atom_charge_.push_back( atom->Charge() * Constants::ELECTOAMBER / sqrt(dielc_) ); - return 0; - } - -diff --git AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py -index e6c4fe9..d7cc7ec 100644 ---- AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py -+++ AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py -@@ -63,7 +63,7 @@ class mmpbsa_data(dict): - self.stability = app.stability - # Now load the data - for key in app.calc_types: -- if key == 'mutant': -+ if key == 'mutant' or key =='qh': - has_mutant = True - continue - self[key] = {} -@@ -86,6 +86,7 @@ class mmpbsa_data(dict): - if has_mutant: - self.mutant = {} - for key in app.calc_types['mutant']: -+ if key == 'qh': continue - self.mutant[key] = {} - tmpdict = {} - for dkey in app.calc_types['mutant'][key]['complex'].data: -diff --git AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py -index ecdc2f2..ecaa6c1 100644 ---- AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py -+++ AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py -@@ -80,6 +80,7 @@ class InfoFile(object): - outfile.write('numframes = %d\n' % self.app.numframes) - outfile.write('numframes_nmode = %d\n' % self.app.numframes_nmode) - outfile.write("mut_str = '%s'\n" % self.app.mut_str) -+ outfile.write('using_chamber = %s\n' % self.app.using_chamber) - outfile.write(self.app.input_file_text) - - def read_info(self, name=None): -diff --git AmberTools/src/parmed/chemistry/__init__.py AmberTools/src/parmed/chemistry/__init__.py -index 52f5245..544e016 100644 ---- AmberTools/src/parmed/chemistry/__init__.py -+++ AmberTools/src/parmed/chemistry/__init__.py -@@ -11,10 +11,14 @@ from chemistry.structure import Structure - from chemistry.topologyobjects import * - from chemistry import unit - from chemistry.residue import * --from chemistry import amber, charmm, tinker, openmm -+from chemistry import amber, charmm, tinker - from chemistry import formats - load_file = formats.load_file - read_PDB = formats.PDBFile.parse - read_CIF = formats.CIFFile.parse - write_PDB = formats.PDBFile.write - write_CIF = formats.CIFFile.write -+try: -+ from chemistry import openmm -+except ImportError: -+ pass -diff --git AmberTools/test/mmpbsa_py/07_Comprehensive/Run.comprehensive AmberTools/test/mmpbsa_py/07_Comprehensive/Run.comprehensive -index 268515e..aa7d9df 100755 ---- AmberTools/test/mmpbsa_py/07_Comprehensive/Run.comprehensive -+++ AmberTools/test/mmpbsa_py/07_Comprehensive/Run.comprehensive -@@ -108,6 +108,24 @@ if [ -z "$DO_PARALLEL" ]; then - ../../dacdif -a 6.0 FINAL_RESULTS_MMPBSA_2.dat.save FINAL_RESULTS_MMPBSA_2.dat - fi - -+# Check the API -+python << EOF -+from __future__ import division -+import MMPBSA_mods.API as API -+ -+print('Checking the API') -+try: -+ stuff = API.load_mmpbsa_info('_MMPBSA_info') -+ total_data = stuff['gb']['complex']['TOTAL'] -+ if abs((sum(total_data) / len(total_data)) + 466.7565) > 0.0002: -+ print('possible FAILURE') -+ else: -+ print('PASSED') -+except: -+ print('Program error') -+print('==============================================================') -+EOF -+ - $EXE --clean 2>&1 > /dev/null - - rm -f mmpbsa.in mmpbsa.out FINAL_DECOMP_MMPBSA_2.csv-e FINAL_DECOMP_MMPBSA.dat diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.2.patch b/sci-chemistry/ambertools/files/ambertools-15-update.2.patch deleted file mode 100644 index b0f1cd978..000000000 --- a/sci-chemistry/ambertools/files/ambertools-15-update.2.patch +++ /dev/null @@ -1,56 +0,0 @@ -*******> update.2 - -Author: Jason Swails, Ross Walker - -Date: June 2, 2015 - -Programs: AmberTools, CUDA - -Description: Adds support for CUDA 7. Also fixes an erroneous error report when - AmberTools is configured for *only* OpenMP, CUDA, or CUDA-MPI with - regards to missing Python modules. - --------------------------------------------------------------------------------- - - AmberTools/src/configure2 | 4 ++-- - AmberTools/test/test_check.sh | 7 ++++--- - 2 files changed, 6 insertions(+), 5 deletions(-) - -diff --git AmberTools/src/configure2 AmberTools/src/configure2 -index f1a3cff..9a504b1 100755 ---- AmberTools/src/configure2 -+++ AmberTools/src/configure2 -@@ -861,13 +861,13 @@ if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPXP" = 'yes' -o "$cuda_DPFP" = 'yes' ]; the - echo "CUDA Version $cudaversion detected" - echo "Configuring for SM2.0 and SM3.0 - warning does not support Maxwell (GM200/GM204) cards [e.g. GTX970/980]" - nvccflags="$sm20flags $sm30flags" -- elif [ "$cudaversion" = "6.5" ]; then -+ elif [ "$cudaversion" = "6.5" -o "$cudaversion" = "7.0" ]; then - echo "CUDA Version $cudaversion detected" - echo "Configuring for SM2.0, SM3.0 and SM5.0" - nvccflags="$sm20flags $sm30flags $sm50flags" - else - echo "Error: Unsupported CUDA version $cudaversion detected." -- echo " AMBER requires CUDA version == 5.0 .or. 5.5 .or. 6.0 .or. 6.5" -+ echo " AMBER requires CUDA version == 5.0 .or. 5.5 .or. 6.0 .or. 6.5 .or. 7.0" - exit 1 - fi - nvcc="$nvcc $nvccflags" -diff --git AmberTools/test/test_check.sh AmberTools/test/test_check.sh -index 108c446..a5399d8 100644 ---- AmberTools/test/test_check.sh -+++ AmberTools/test/test_check.sh -@@ -83,9 +83,10 @@ def error(): - try: - import chemistry - except ImportError: -- sys.stderr.write('Could not import Amber Python modules. This likely means\\n' -- 'that your Amber Python environment was not set up correctly\\n\\n') -- error() -+ if os.path.exists(os.path.join(ambhome, 'parmed.py')): -+ sys.stderr.write('Could not import Amber Python modules. This likely means\\n' -+ 'that your Amber Python environment was not set up correctly\\n\\n') -+ error() - - if 'darwin' in sys.platform: - sys.exit(0) # Nothing to check here diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.3.patch b/sci-chemistry/ambertools/files/ambertools-15-update.3.patch deleted file mode 100644 index a892ecefd..000000000 --- a/sci-chemistry/ambertools/files/ambertools-15-update.3.patch +++ /dev/null @@ -1,95 +0,0 @@ -********> update.3 - Author: Istvan Kolossvary - Date: 15 June 2015 - - Programs: nab, sff - - Description: Fix problem with lmod docking when fixed atoms are present - - --------------------------------------------------------------------------- - -diff --git AmberTools/src/sff/lmodC.c AmberTools/src/sff/lmodC.c -index 8a19dd8..45c8244 100644 ---- AmberTools/src/sff/lmodC.c -+++ AmberTools/src/sff/lmodC.c -@@ -864,7 +864,7 @@ trans_ligand(double *xyz, int start, int end, double dx, double dy, - double dz) - { - int i, x, y, z; -- for (i = start - 1; i < end; i++) { -+ for (i = start; i <= end; i++) { - x = 3 * i; - y = x + 1; - z = y + 1; -@@ -900,7 +900,7 @@ rot_ligand(double *xyz, int start, int end, double cent_x, double cent_y, - { - int i, x, y, z; - double temp_x, temp_y, temp_z; -- for (i = start - 1; i < end; i++) { -+ for (i = start; i <= end; i++) { - x = 3 * i; - y = x + 1; - z = y + 1; -@@ -930,7 +930,7 @@ calc_centroid(double *xyz, int start, int end, double *cent_x, - { - int i, x, y, z, n; - *cent_x = *cent_y = *cent_z = ZERO; -- for (i = start - 1; i < end; i++) { -+ for (i = start; i <= end; i++) { - x = 3 * i; - y = x + 1; - z = y + 1; -@@ -1591,6 +1591,7 @@ lmodC(int *nlmodit, int *nmod, int *kmod, int *rotran, int *natm_ext, - i, j, k, kk, l, n, cnt; - static int barrier_crossing_test_on, do_all, do_ligs; - static int *index = NULL; -+ static int ikk, lig_start_kk, lig_end_kk, lig_rot_cent_kk; - static double ref_energy, energy, energy_old, min_energy, - glob_min_energy, rad, sum, max_atmov, scale, lmod_step, rms, - rms_old, grad_rms; -@@ -2554,7 +2555,19 @@ lmodC(int *nlmodit, int *nmod, int *kmod, int *rotran, int *natm_ext, - xtrans *= trscale / trnorm; - ytrans *= trscale / trnorm; - ztrans *= trscale / trnorm; -- trans_ligand(xyz_local, lig_start[kk], lig_end[kk], xtrans, -+ for (ikk = 0; ikk < natm_local; ikk++ ) { -+ if ( atm_indx[ikk] == (lig_start[kk] -1) ) { /* lig_start[] contains external PDB atom numbers */ -+ lig_start_kk = ikk; -+ break; -+ } -+ } -+ for (ikk = 0; ikk < natm_local; ikk++ ) { -+ if ( atm_indx[ikk] == (lig_end[kk] -1) ) { /* lig_end[] contains external PDB atom numbers */ -+ lig_end_kk = ikk; -+ break; -+ } -+ } -+ trans_ligand(xyz_local, lig_start_kk, lig_end_kk, xtrans, - ytrans, ztrans); - do { - xrot = 2 * rand2() - 1; -@@ -2568,13 +2581,19 @@ lmodC(int *nlmodit, int *nmod, int *kmod, int *rotran, int *natm_ext, - rotang = angmin[kk] + (angmax[kk] - angmin[kk]) * rand2(); - calc_rot_matrix(DEG2RAD * rotang, xrot, yrot, zrot, rotmat); - if (lig_rot_cent[kk]) { -- xcent = xyz_local[(lig_rot_cent[kk] - 1) * 3 ]; -- ycent = xyz_local[(lig_rot_cent[kk] - 1) * 3 + 1]; -- zcent = xyz_local[(lig_rot_cent[kk] - 1) * 3 + 2]; -+ for (ikk = 0; ikk < natm_local; ikk++ ) { -+ if ( atm_indx[ikk] == (lig_rot_cent[kk] -1) ) { /* lig_rot_cent[] contains external PDB atom numbers */ -+ lig_rot_cent_kk = ikk; -+ break; -+ } -+ } -+ xcent = xyz_local[ lig_rot_cent_kk * 3 ]; -+ ycent = xyz_local[ lig_rot_cent_kk * 3 + 1]; -+ zcent = xyz_local[ lig_rot_cent_kk * 3 + 2]; - } else -- calc_centroid(xyz_local, lig_start[kk], lig_end[kk], -+ calc_centroid(xyz_local, lig_start_kk, lig_end_kk, - &xcent, &ycent, &zcent); -- rot_ligand(xyz_local, lig_start[kk], lig_end[kk], xcent, -+ rot_ligand(xyz_local, lig_start_kk, lig_end_kk, xcent, - ycent, zcent, rotmat); - } - /* close pair separation operates on xyz_ext[]: */ diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.4.patch b/sci-chemistry/ambertools/files/ambertools-15-update.4.patch deleted file mode 100644 index 4176a583a..000000000 --- a/sci-chemistry/ambertools/files/ambertools-15-update.4.patch +++ /dev/null @@ -1,908 +0,0 @@ -*******> update.4 -Author: Benjamin D. Madej -Date: October 19, 2015 -Programs: Leap, Lipid14 force field -Description: Adds a parameter set for cholesterol to the Lipid14 force field. - Please reference: - Madej, B. D.; Gould, I.R.; Walker, R. C. A Parameterization of - Cholesterol for Mixed Lipid Bilayer Simulation within the Amber - Lipid14 Force Field. J. Phys. Chem. B 2015, 119 (38) - pp 12424-12435. -------------------------------------------------------------------------------- - dat/leap/lib/lipid14.lib | 480 ++++++++++++++++++++++++++++++++++++++++++++++ - dat/leap/parm/lipid11.dat | 2 +- - dat/leap/parm/lipid14.dat | 291 ++++++++++++++++++---------- - 3 files changed, 666 insertions(+), 107 deletions(-) - -diff --git dat/leap/lib/lipid14.lib dat/leap/lib/lipid14.lib -index 891937b..75c2f2b 100644 ---- dat/leap/lib/lipid14.lib -+++ dat/leap/lib/lipid14.lib -@@ -1,10 +1,490 @@ - !!index array str -+ "CHL" - "LA" - "MY" - "OL" - "PA" - "PC" - "PE" -+!entry.CHL.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg -+ "C1" "cA" 0 1 131073 1 6 -0.031691 -+ "H11" "hA" 0 1 131073 2 1 0.009380 -+ "H12" "hA" 0 1 131073 3 1 0.009380 -+ "C2" "cA" 0 1 131073 4 6 -0.088130 -+ "H21" "hA" 0 1 131073 5 1 0.044625 -+ "H22" "hA" 0 1 131073 6 1 0.044625 -+ "C3" "cA" 0 1 131073 7 6 0.293553 -+ "H31" "hE" 0 1 131073 8 1 0.029611 -+ "C4" "cA" 0 1 131073 9 6 -0.162218 -+ "H41" "hA" 0 1 131073 10 1 0.090036 -+ "H42" "hA" 0 1 131073 11 1 0.090036 -+ "C5" "cB" 0 1 131073 12 6 -0.139495 -+ "C6" "cB" 0 1 131073 13 6 -0.208190 -+ "H61" "hB" 0 1 131073 14 1 0.122828 -+ "C7" "cA" 0 1 131073 15 6 -0.069897 -+ "H71" "hA" 0 1 131073 16 1 0.047919 -+ "H72" "hA" 0 1 131073 17 1 0.047919 -+ "C8" "cA" 0 1 131073 18 6 -0.011390 -+ "H81" "hA" 0 1 131073 19 1 0.072891 -+ "C9" "cA" 0 1 131073 20 6 0.019609 -+ "H91" "hA" 0 1 131073 21 1 0.029289 -+ "C10" "cA" 0 1 131073 22 6 0.079112 -+ "C11" "cA" 0 1 131073 23 6 -0.066365 -+ "H111" "hA" 0 1 131073 24 1 0.030085 -+ "H112" "hA" 0 1 131073 25 1 0.030085 -+ "C12" "cA" 0 1 131073 26 6 -0.064973 -+ "H121" "hA" 0 1 131073 27 1 0.010352 -+ "H122" "hA" 0 1 131073 28 1 0.010352 -+ "C13" "cA" 0 1 131073 29 6 0.057407 -+ "C14" "cA" 0 1 131073 30 6 0.005830 -+ "H141" "hA" 0 1 131073 31 1 0.031557 -+ "C15" "cA" 0 1 131073 32 6 -0.101977 -+ "H151" "hA" 0 1 131073 33 1 0.026458 -+ "H152" "hA" 0 1 131073 34 1 0.026458 -+ "C16" "cA" 0 1 131073 35 6 -0.092064 -+ "H161" "hA" 0 1 131073 36 1 0.033335 -+ "H162" "hA" 0 1 131073 37 1 0.033335 -+ "C17" "cA" 0 1 131073 38 6 0.032398 -+ "H171" "hA" 0 1 131073 39 1 0.016590 -+ "C18" "cA" 0 1 131073 40 6 -0.115049 -+ "H181" "hA" 0 1 131073 41 1 0.024541 -+ "H182" "hA" 0 1 131073 42 1 0.024541 -+ "H183" "hA" 0 1 131073 43 1 0.024541 -+ "C19" "cA" 0 1 131073 44 6 -0.108064 -+ "H191" "hA" 0 1 131073 45 1 0.033990 -+ "H192" "hA" 0 1 131073 46 1 0.033990 -+ "H193" "hA" 0 1 131073 47 1 0.033990 -+ "C20" "cD" 0 1 131075 48 6 0.044268 -+ "H201" "hL" 0 1 131075 49 1 0.020951 -+ "C21" "cD" 0 1 131075 50 6 -0.154621 -+ "H211" "hL" 0 1 131075 51 1 0.036274 -+ "H212" "hL" 0 1 131075 52 1 0.036274 -+ "H213" "hL" 0 1 131075 53 1 0.036274 -+ "C22" "cD" 0 1 131075 54 6 -0.039033 -+ "H221" "hL" 0 1 131075 55 1 0.008359 -+ "H222" "hL" 0 1 131075 56 1 0.008359 -+ "C23" "cD" 0 1 131075 57 6 -0.028460 -+ "H231" "hL" 0 1 131075 58 1 0.015742 -+ "H232" "hL" 0 1 131075 59 1 0.015742 -+ "C24" "cD" 0 1 131075 60 6 -0.125596 -+ "H241" "hL" 0 1 131075 61 1 0.040110 -+ "H242" "hL" 0 1 131075 62 1 0.040110 -+ "C25" "cD" 0 1 131075 63 6 0.212446 -+ "H251" "hL" 0 1 131075 64 1 -0.002466 -+ "C26" "cD" 0 1 131075 65 6 -0.257776 -+ "H261" "hL" 0 1 131075 66 1 0.057982 -+ "H262" "hL" 0 1 131075 67 1 0.057982 -+ "H263" "hL" 0 1 131075 68 1 0.057982 -+ "C27" "cD" 0 1 131075 69 6 -0.257776 -+ "H271" "hL" 0 1 131075 70 1 0.057982 -+ "H272" "hL" 0 1 131075 71 1 0.057982 -+ "H273" "hL" 0 1 131075 72 1 0.057982 -+ "O1" "oH" 0 1 131073 73 8 -0.703022 -+ "HO1" "hO" 0 1 131073 74 1 0.414804 -+!entry.CHL.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg -+ "C1" "cA" 0 -1 0.0 -+ "H11" "hA" 0 -1 0.0 -+ "H12" "hA" 0 -1 0.0 -+ "C2" "cA" 0 -1 0.0 -+ "H21" "hA" 0 -1 0.0 -+ "H22" "hA" 0 -1 0.0 -+ "C3" "cA" 0 -1 0.0 -+ "H31" "hE" 0 -1 0.0 -+ "C4" "cA" 0 -1 0.0 -+ "H41" "hA" 0 -1 0.0 -+ "H42" "hA" 0 -1 0.0 -+ "C5" "cB" 0 -1 0.0 -+ "C6" "cB" 0 -1 0.0 -+ "H61" "hB" 0 -1 0.0 -+ "C7" "cA" 0 -1 0.0 -+ "H71" "hA" 0 -1 0.0 -+ "H72" "hA" 0 -1 0.0 -+ "C8" "cA" 0 -1 0.0 -+ "H81" "hA" 0 -1 0.0 -+ "C9" "cA" 0 -1 0.0 -+ "H91" "hA" 0 -1 0.0 -+ "C10" "cA" 0 -1 0.0 -+ "C11" "cA" 0 -1 0.0 -+ "H111" "hA" 0 -1 0.0 -+ "H112" "hA" 0 -1 0.0 -+ "C12" "cA" 0 -1 0.0 -+ "H121" "hA" 0 -1 0.0 -+ "H122" "hA" 0 -1 0.0 -+ "C13" "cA" 0 -1 0.0 -+ "C14" "cA" 0 -1 0.0 -+ "H141" "hA" 0 -1 0.0 -+ "C15" "cA" 0 -1 0.0 -+ "H151" "hA" 0 -1 0.0 -+ "H152" "hA" 0 -1 0.0 -+ "C16" "cA" 0 -1 0.0 -+ "H161" "hA" 0 -1 0.0 -+ "H162" "hA" 0 -1 0.0 -+ "C17" "cA" 0 -1 0.0 -+ "H171" "hA" 0 -1 0.0 -+ "C18" "cA" 0 -1 0.0 -+ "H181" "hA" 0 -1 0.0 -+ "H182" "hA" 0 -1 0.0 -+ "H183" "hA" 0 -1 0.0 -+ "C19" "cA" 0 -1 0.0 -+ "H191" "hA" 0 -1 0.0 -+ "H192" "hA" 0 -1 0.0 -+ "H193" "hA" 0 -1 0.0 -+ "C20" "cA" 0 -1 0.0 -+ "H201" "hA" 0 -1 0.0 -+ "C21" "cA" 0 -1 0.0 -+ "H211" "hA" 0 -1 0.0 -+ "H212" "hA" 0 -1 0.0 -+ "H213" "hA" 0 -1 0.0 -+ "C22" "cA" 0 -1 0.0 -+ "H221" "hA" 0 -1 0.0 -+ "H222" "hA" 0 -1 0.0 -+ "C23" "cA" 0 -1 0.0 -+ "H231" "hA" 0 -1 0.0 -+ "H232" "hA" 0 -1 0.0 -+ "C24" "cA" 0 -1 0.0 -+ "H241" "hA" 0 -1 0.0 -+ "H242" "hA" 0 -1 0.0 -+ "C25" "cA" 0 -1 0.0 -+ "H251" "hA" 0 -1 0.0 -+ "C26" "cA" 0 -1 0.0 -+ "H261" "hA" 0 -1 0.0 -+ "H262" "hA" 0 -1 0.0 -+ "H263" "hA" 0 -1 0.0 -+ "C27" "cA" 0 -1 0.0 -+ "H271" "hA" 0 -1 0.0 -+ "H272" "hA" 0 -1 0.0 -+ "H273" "hA" 0 -1 0.0 -+ "O1" "oH" 0 -1 0.0 -+ "HO1" "hO" 0 -1 0.0 -+!entry.CHL.unit.boundbox array dbl -+ -1.000000 -+ 0.0 -+ 0.0 -+ 0.0 -+ 0.0 -+!entry.CHL.unit.childsequence single int -+ 2 -+!entry.CHL.unit.connect array int -+ 0 -+ 0 -+!entry.CHL.unit.connectivity table int atom1x int atom2x int flags -+ 1 2 1 -+ 1 3 1 -+ 1 4 1 -+ 1 22 1 -+ 4 5 1 -+ 4 6 1 -+ 4 7 1 -+ 7 8 1 -+ 7 9 1 -+ 7 73 1 -+ 9 10 1 -+ 9 11 1 -+ 9 12 1 -+ 12 13 2 -+ 12 22 1 -+ 13 14 1 -+ 13 15 1 -+ 15 16 1 -+ 15 17 1 -+ 15 18 1 -+ 18 19 1 -+ 18 20 1 -+ 18 30 1 -+ 20 21 1 -+ 20 22 1 -+ 20 23 1 -+ 22 44 1 -+ 23 24 1 -+ 23 25 1 -+ 23 26 1 -+ 26 27 1 -+ 26 28 1 -+ 26 29 1 -+ 29 30 1 -+ 29 38 1 -+ 29 40 1 -+ 30 31 1 -+ 30 32 1 -+ 32 33 1 -+ 32 34 1 -+ 32 35 1 -+ 35 36 1 -+ 35 37 1 -+ 35 38 1 -+ 38 39 1 -+ 38 48 1 -+ 40 41 1 -+ 40 42 1 -+ 40 43 1 -+ 44 45 1 -+ 44 46 1 -+ 44 47 1 -+ 48 49 1 -+ 48 50 1 -+ 48 54 1 -+ 50 51 1 -+ 50 52 1 -+ 50 53 1 -+ 54 55 1 -+ 54 56 1 -+ 54 57 1 -+ 57 58 1 -+ 57 59 1 -+ 57 60 1 -+ 60 61 1 -+ 60 62 1 -+ 60 63 1 -+ 63 64 1 -+ 63 65 1 -+ 63 69 1 -+ 65 66 1 -+ 65 67 1 -+ 65 68 1 -+ 69 70 1 -+ 69 71 1 -+ 69 72 1 -+ 73 74 1 -+!entry.CHL.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 -+ "R" 1 "A" 27 -+ "R" 1 "A" 28 -+ "R" 1 "A" 29 -+ "R" 1 "A" 30 -+ "R" 1 "A" 31 -+ "R" 1 "A" 32 -+ "R" 1 "A" 33 -+ "R" 1 "A" 34 -+ "R" 1 "A" 35 -+ "R" 1 "A" 36 -+ "R" 1 "A" 37 -+ "R" 1 "A" 38 -+ "R" 1 "A" 39 -+ "R" 1 "A" 40 -+ "R" 1 "A" 41 -+ "R" 1 "A" 42 -+ "R" 1 "A" 43 -+ "R" 1 "A" 44 -+ "R" 1 "A" 45 -+ "R" 1 "A" 46 -+ "R" 1 "A" 47 -+ "R" 1 "A" 48 -+ "R" 1 "A" 49 -+ "R" 1 "A" 50 -+ "R" 1 "A" 51 -+ "R" 1 "A" 52 -+ "R" 1 "A" 53 -+ "R" 1 "A" 54 -+ "R" 1 "A" 55 -+ "R" 1 "A" 56 -+ "R" 1 "A" 57 -+ "R" 1 "A" 58 -+ "R" 1 "A" 59 -+ "R" 1 "A" 60 -+ "R" 1 "A" 61 -+ "R" 1 "A" 62 -+ "R" 1 "A" 63 -+ "R" 1 "A" 64 -+ "R" 1 "A" 65 -+ "R" 1 "A" 66 -+ "R" 1 "A" 67 -+ "R" 1 "A" 68 -+ "R" 1 "A" 69 -+ "R" 1 "A" 70 -+ "R" 1 "A" 71 -+ "R" 1 "A" 72 -+ "R" 1 "A" 73 -+ "R" 1 "A" 74 -+!entry.CHL.unit.name single str -+ "CHL" -+!entry.CHL.unit.positions table dbl x dbl y dbl z -+ 4.697000 -1.469000 -0.739000 -+ 4.428000 -1.214000 -1.762000 -+ 4.303000 -2.462000 -0.556000 -+ 6.224000 -1.517000 -0.642000 -+ 6.547000 -1.874000 0.331000 -+ 6.617000 -2.214000 -1.376000 -+ 6.830000 -0.145000 -0.877000 -+ 6.590000 0.176000 -1.891000 -+ 6.246000 0.863000 0.111000 -+ 6.601000 0.589000 1.102000 -+ 6.636000 1.856000 -0.095000 -+ 4.731000 0.895000 0.070000 -+ 4.091000 2.041000 -0.088000 -+ 4.668000 2.946000 -0.204000 -+ 2.599000 2.206000 -0.119000 -+ 2.323000 3.070000 0.480000 -+ 2.290000 2.443000 -1.137000 -+ 1.853000 0.964000 0.375000 -+ 1.922000 0.946000 1.460000 -+ 2.514000 -0.306000 -0.204000 -+ 2.518000 -0.165000 -1.285000 -+ 4.012000 -0.452000 0.214000 -+ 1.671000 -1.566000 0.076000 -+ 2.085000 -2.410000 -0.467000 -+ 1.730000 -1.829000 1.125000 -+ 0.190000 -1.429000 -0.312000 -+ 0.108000 -1.322000 -1.392000 -+ -0.312000 -2.355000 -0.056000 -+ -0.469000 -0.212000 0.358000 -+ 0.381000 1.015000 -0.041000 -+ 0.381000 1.020000 -1.132000 -+ -0.462000 2.215000 0.391000 -+ -0.304000 2.443000 1.442000 -+ -0.217000 3.115000 -0.163000 -+ -1.913000 1.751000 0.131000 -+ -2.537000 1.930000 1.001000 -+ -2.357000 2.309000 -0.684000 -+ -1.859000 0.228000 -0.203000 -+ -1.794000 0.127000 -1.286000 -+ -0.546000 -0.407000 1.886000 -+ -1.062000 0.412000 2.374000 -+ 0.431000 -0.485000 2.344000 -+ -1.086000 -1.316000 2.130000 -+ 4.156000 -0.937000 1.675000 -+ 3.579000 -0.319000 2.354000 -+ 5.185000 -0.898000 2.008000 -+ 3.826000 -1.963000 1.788000 -+ -3.141000 -0.519000 0.237000 -+ -3.267000 -0.372000 1.309000 -+ -3.080000 -2.029000 -0.029000 -+ -2.330000 -2.520000 0.577000 -+ -2.851000 -2.232000 -1.072000 -+ -4.025000 -2.508000 0.198000 -+ -4.375000 0.093000 -0.461000 -+ -4.324000 1.175000 -0.403000 -+ -4.337000 -0.153000 -1.522000 -+ -5.732000 -0.335000 0.111000 -+ -5.862000 -1.406000 0.010000 -+ -5.752000 -0.121000 1.179000 -+ -6.898000 0.389000 -0.569000 -+ -6.718000 1.461000 -0.516000 -+ -6.910000 0.137000 -1.629000 -+ -8.286000 0.104000 0.028000 -+ -8.244000 0.333000 1.092000 -+ -8.705000 -1.362000 -0.122000 -+ -8.034000 -2.035000 0.400000 -+ -8.723000 -1.655000 -1.169000 -+ -9.702000 -1.521000 0.280000 -+ -9.336000 1.023000 -0.605000 -+ -9.079000 2.069000 -0.470000 -+ -10.316000 0.862000 -0.166000 -+ -9.420000 0.839000 -1.674000 -+ 8.224000 -0.262000 -0.734000 -+ 8.633000 0.570000 -0.924000 -+!entry.CHL.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -+ 0 0 0 0 0 0 -+!entry.CHL.unit.residues table str name int seq int childseq int startatomx str restype int imagingx -+ "CHL" 1 75 1 "?" 0 -+!entry.CHL.unit.residuesPdbSequenceNumber array int -+ 0 -+!entry.CHL.unit.solventcap array dbl -+ -1.000000 -+ 0.0 -+ 0.0 -+ 0.0 -+ 0.0 -+!entry.CHL.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 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 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.LA.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg - "H12T" "hL" 0 1 131073 1 1 0.025809 - "C112" "cD" 0 1 131073 2 6 -0.118534 -diff --git dat/leap/parm/lipid11.dat dat/leap/parm/lipid11.dat -index 0f8d83e..9c25f35 100644 ---- dat/leap/parm/lipid11.dat -+++ dat/leap/parm/lipid11.dat -@@ -1,4 +1,4 @@ --AMBER Lipid 2011 Force Field (v1.0), A.Skjevik, B. Madej, K.Teigen & R.C.Walker -+** Warning: Lipid11 is deprecated. Please refer to Amber Lipid14 for more information ** AMBER Lipid 2011 Force Field (v1.0), A.Skjevik, B. Madej, K.Teigen & R.C.Walker - cC 12.01 carbonyl sp2 carbon (GAFF c -) - cB 12.01 aliphatic sp2 carbon (GAFF c2-) - cA 12.01 sp3 carbon (GAFF c3-) -diff --git dat/leap/parm/lipid14.dat dat/leap/parm/lipid14.dat -index 46da737..f102976 100644 ---- dat/leap/parm/lipid14.dat -+++ dat/leap/parm/lipid14.dat -@@ -3,59 +3,81 @@ cA 12.01 sp3 carbon (GAFF c3-head,glycerol) - cB 12.01 aliphatic sp2 carbon (GAFF c2-tail) - cC 12.01 carbonyl sp2 carbon (GAFF c -head,glycerol) - cD 12.010 sp3 carbon (GAFFlipid a3-tail) -+hA 1.008 H bonded to aliphatic carbon without electrwd. group (GAFF hc-) -+hB 1.008 H bonded to aromatic carbon (GAFF ha-) -+hE 1.008 H bonded to aliphatic carbon with 1 electrwd. group (GAFF h1-) -+hL 1.008 H bonded to aliphatic carbon without electrwd. group (GAFFlipid hl-) -+hN 1.008 H bonded to nitrogen (GAFF hn-) -+hO 1.008 H in Hydroxyl group (GAFF ho-) -+hX 1.008 H bonded to C next to positively charged group (GAFF hx-) -+nA 14.01 sp3 N with four connected atoms (GAFF n4-) - oC 16.00 sp2 oxygen with one connected atom (e.g C=O, COO-) (GAFF o -) --oS 16.00 sp3 oxygen in ethers and esters (GAFF os-) -+oH 16.00 sp3 oxygen in hydroxyl group (GAFF oh-) - oP 16.00 sp2 oxygen with one connected atom (e.g P-O) in phosphate group (GAFF o -) -+oS 16.00 sp3 oxygen in ethers and esters (GAFF os-) - oT 16.00 sp3 oxygen bonded to carbon in phosphate group (GAFF os-) --nA 14.01 sp3 N with four connected atoms (GAFF n4-) - pA 30.97 phosphorus with four connected atoms, such as O=P(OH)3 (GAFF p5-) --hE 1.008 H bonded to aliphatic carbon with 1 electrwd. group (GAFF h1-) --hX 1.008 H bonded to C next to positively charged group (GAFF hx-) --hB 1.008 H bonded to aromatic carbon (GAFF ha-) --hN 1.008 H bonded to nitrogen (GAFF hn-) --hL 1.008 H bonded to aliphatic carbon without electrwd. group (GAFFlipid hl-) - - cA cB cC cD oC oS oP oT nA pA hE hX hB hN hL - cA-cA 303.1 1.5350 Lipid11 v1.0 (GAFF c3-c3) -+cA-cB 328.3 1.5080 Lipid11 v1.0 (GAFF c3-c2) -+cA-cD 303.1 1.5350 Lipid14 v2.14(GAFF c3-c3) -+cA-hA 337.3 1.0920 Lipid11 v1.0 (GAFF c3-hc) - cA-hE 335.9 1.0930 Lipid11 v1.0 (GAFF c3-h1) - cA-hX 338.7 1.0910 Lipid11 v1.0 (GAFF c3-hx) - cA-nA 293.6 1.4990 Lipid11 v1.0 (GAFF c3-n4) -+cA-oH 314.1 1.4260 Lipid11 v1.0 (GAFF c3-oh) - cA-oS 301.5 1.4390 Lipid11 v1.0 (GAFF c3-os) - cA-oT 301.5 1.4390 Lipid11 v1.0 (GAFF c3-os) - cB-cB 589.7 1.3240 Lipid11 v1.0 (GAFF c2-c2) -+cB-cD 328.3 1.5080 Lipid14 v2.0 (GAFF c2-c3) - cB-hB 344.3 1.0870 Lipid11 v1.0 (GAFF c2-ha) -+cC-cD 328.3 1.5080 Lipid14 v2.0 (GAFF c -c3) - cC-oC 648.0 1.2140 Lipid11 v1.0 (GAFF c -o ) - cC-oS 411.3 1.3430 Lipid11 v1.0 (GAFF c -os) --cD-cB 328.3 1.5080 Lipid14 v2.0 (GAFF c3-c2) --cD-cC 328.3 1.5080 Lipid14 v2.0 (GAFF c3-c ) - cD-cD 303.1 1.5350 Lipid14 v2.0 (GAFF c3-c3) - cD-hL 337.3 1.0920 Lipid14 v2.0 (GAFF c3-hc) - hN-nA 369.0 1.0330 Lipid11 v1.0 (GAFF hn-n4) -+hO-oH 369.6 0.9740 Lipid11 v1.0 (GAFF ho-oh) - oP-pA 487.7 1.4810 Lipid11 v1.0 (GAFF o -p5) - oT-pA 342.5 1.6020 Lipid11 v1.0 (GAFF os-p5) - - cA-cA-cA 63.210 110.630 Lipid11 v1.0 (GAFF c3-c3-c3) -+cA-cA-cB 63.530 111.440 Lipid11 v1.0 (GAFF c3-c3-c2) -+cA-cA-cD 63.210 110.630 Lipid14 v2.14(GAFF c3-c3-c3) -+cA-cA-hA 46.370 110.050 Lipid11 v1.0 (GAFF c3-c3-hc) - cA-cA-hE 46.360 110.070 Lipid11 v1.0 (GAFF c3-c3-h1) - cA-cA-hX 46.020 111.740 Lipid11 v1.0 (GAFF c3-c3-hx) - cA-cA-nA 64.450 114.320 Lipid11 v1.0 (GAFF c3-c3-n4) -+cA-cA-oH 67.720 109.430 Lipid11 v1.0 (GAFF c3-c3-oh) - cA-cA-oS 67.780 108.420 Lipid11 v1.0 (GAFF c3-c3-os) - cA-cA-oT 67.780 108.420 Lipid11 v1.0 (GAFF c3-c3-os) -+cA-cB-cA 62.700 116.520 Lipid11 v1.0 (GAFF c3-c2-c3) -+cA-cB-cB 64.330 123.420 Lipid11 v1.0 (GAFF c3-c2-c2) -+cA-cB-hB 45.660 117.300 Lipid11 v1.0 (GAFF c3-c2-ha) -+cA-cD-cD 63.210 110.630 Lipid14 v2.14(GAFF c3-c3-c3) -+cA-cD-hL 46.370 110.050 Lipid14 v2.14(GAFF c3-c3-hc) - cA-nA-cA 62.840 110.640 Lipid11 v1.0 (GAFF c3-n4-c3) - cA-nA-hN 46.190 110.110 Lipid11 v1.0 (GAFF c3-n4-hn) -+cA-oH-hO 47.090 108.160 Lipid11 v1.0 (GAFF c3-oh-ho) - cA-oS-cC 63.630 115.140 Lipid11 v1.0 (GAFF c3-os-c ) - cA-oT-pA 78.480 118.000 Lipid11 v1.0 (GAFF c3-os-p5) -+cB-cA-hA 47.030 110.490 Lipid11 v1.0 (GAFF c2-c3-hc) -+cB-cB-cD 64.330 123.420 Lipid14 v2.0 (GAFF c2-c2-c3) - cB-cB-hB 50.040 120.940 Lipid11 v1.0 (GAFF c2-c2-ha) -+cB-cD-cD 63.530 111.440 Lipid14 v2.0 (GAFF c2-c3-c3) - cB-cD-hL 47.030 110.490 Lipid14 v2.0 (GAFF c2-c3-hc) -+cC-cD-cD 63.790 110.530 Lipid14 v2.0 (GAFF c -c3-c3) - cC-cD-hL 47.200 109.680 Lipid14 v2.0 (GAFF c -c3-hc) --cD-cB-cB 64.330 123.420 Lipid14 v2.0 (GAFF c3-c2-c2) -+cD-cA-hA 46.370 110.050 Lipid14 v2.14(GAFF c3-c3-hc) - cD-cB-hB 45.660 117.300 Lipid14 v2.0 (GAFF c3-c2-ha) - cD-cC-oC 68.030 123.110 Lipid14 v2.0 (GAFF c3-c -o ) - cD-cC-oS 69.260 111.960 Lipid14 v2.0 (GAFF c3-c -os) --cD-cD-cB 63.530 111.440 Lipid14 v2.0 (GAFF c3-c3-c2) --cD-cD-cC 63.790 110.530 Lipid14 v2.0 (GAFF c3-c3-c ) - cD-cD-cD 63.210 110.630 Lipid14 v2.0 (GAFF c3-c3-c3) - cD-cD-hL 46.370 110.050 Lipid14 v2.0 (GAFF c3-c3-hc) -+hA-cA-hA 39.430 108.350 Lipid11 v1.0 (GAFF hc-c3-hc) - hE-cA-hE 39.180 109.550 Lipid11 v1.0 (GAFF h1-c3-h1) -+hE-cA-oH 50.970 109.880 Lipid11 v1.0 (GAFF ha-c3-oh) - hE-cA-oS 50.840 108.820 Lipid11 v1.0 (GAFF h1-c3-os) - hE-cA-oT 50.840 108.820 Lipid11 v1.0 (GAFF h1-c3-os) - hL-cD-hL 39.430 108.350 Lipid14 v2.0 (GAFF hc-c3-hc) -@@ -67,86 +89,133 @@ oP-pA-oP 46.010 115.800 Lipid11 v1.0 (GAFF o -p5-o ) - oP-pA-oT 44.010 116.090 Lipid11 v1.0 (GAFF o -p5-os) - oT-pA-oT 45.370 101.770 Lipid11 v1.0 (GAFF os-p5-os) - --cA-cA-cA-hE 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) --cA-cA-cA-oS 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) --cA-cA-cA-oT 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) --cA-cA-nA-cA 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X ) --cA-cA-nA-hN 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X ) --cA-cA-oT-pA 1 0.3833 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-os-X ) --cA-nA-cA-hX 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X ) --cA-oS-cC-oS 1 2.700 180.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c -os-X ) --cA-oT-pA-oP 1 0.800 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -os-p5-X ) --cA-oT-pA-oP 1 0.800 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -os-p5-X ) --cA-oT-pA-oT 1 0.25 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-p5-os) --cA-oT-pA-oT 1 1.20 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-p5-os) --cB-cB-cD-cD 1 0.3464 0.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cB-cD-cD 1 -0.5577 0.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cB-cD-cD 1 -0.2920 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cB-cD-cD 1 -0.0943 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cB-cD-cD 1 0.0226 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cD-cD-cD 1 0.0251 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cD-cD-cD 1 0.0054 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cD-cD-cD 1 0.2007 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cD-cD-cD 1 0.2103 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cD-cD-cD 1 0.0811 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cD-cD-hL 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c3-X ) --cC-cD-cD-hL 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c3-X ) --cC-oS-cA-cA 1 0.383 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-os-c ) --cC-oS-cA-cA 1 0.80 180.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-os-c ) --cC-oS-cA-hE 1 0.3833 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-os-X ) --cD-cB-cB-cD 1 0.3073 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cB-cB-cD 1 4.0051 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cB-cB-cD 1 0.1990 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cB-cB-cD 1 0.3242 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cB-cB-cD 1 -0.0415 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cB-cB-hB 1 6.650 180.0 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c2-c2-X ) --cD-cC-oS-cA 1 2.700 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c -os-X ) --cD-cD-cC-oC 1 -0.9110 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cC-oC 1 0.7382 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cC-oC 1 0.3290 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cC-oC 1 -0.5864 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cC-oC 1 0.1333 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cC-oS 1 -0.1226 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cC-oS 1 -0.2054 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cC-oS 1 0.1802 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cC-oS 1 0.5107 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cC-oS 1 0.1355 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cD-cC 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF ) --cD-cD-cD-cD 1 0.3112 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cD-cD 1 -0.1233 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cD-cD 1 0.1149 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cD-cD 1 -0.2199 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cD-cD 1 0.2170 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cD-hL 1 0.16 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF c3-c3-c3-hc) --hB-cB-cB-hB 1 6.650 180.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c2-c2-X ) --hE-cA-cA-hE 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) --hE-cA-cA-nA 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) --hE-cA-cA-hX 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) --hE-cA-cA-oS 1 0.00 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os) --hE-cA-cA-oS 1 0.25 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os) --hE-cA-cA-oT 1 0.00 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os) --hE-cA-cA-oT 1 0.25 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os) --hE-cA-oT-pA 1 0.3833 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-os-X ) --hB-cB-cD-cD 1 0.000 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c2-X ) --hB-cB-cD-hL 1 0.000 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c2-X ) --hL-cD-cB-cB 1 0.38 180.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c2-c2) --hL-cD-cB-cB 1 1.15 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c2-c2) --hL-cD-cC-oC 1 0.80 0.0 -1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c -o ) --hL-cD-cC-oC 1 0.08 180.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c -o ) --hL-cD-cC-oS 1 0.000 180.0 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c -c3-X ) --hL-cD-cD-hL 1 0.15 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c3-hc) --hN-nA-cA-hX 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X ) --hX-cA-cA-oT 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) --nA-cA-cA-oT 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) --cA-oS-cC-oC 1 2.70 180.0 -2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-c -o ) --cA-oS-cC-oC 1 1.40 180.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-c -o ) --oS-cA-cA-oS 1 0.144 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os) --oS-cA-cA-oS 1 1.175 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os) --oT-cA-cA-oS 1 0.144 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os) --oT-cA-cA-oS 1 1.175 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os) -- -+cA-cA-cA-cA 1 0.18 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-c3-c3) -+cA-cA-cA-cA 1 0.25 180.0 -2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-c3-c3) -+cA-cA-cA-cA 1 0.20 180.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-c3-c3) -+cA-cA-cA-cB 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+cA-cA-cA-cD 1 0.3112 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cA-cD 1 -0.1233 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cA-cD 1 0.1149 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cA-cD 1 -0.2199 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cA-cD 1 0.2170 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cA-hA 1 0.16 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-c3-hc) -+cA-cA-cA-hE 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+cA-cA-cA-oH 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+cA-cA-cA-oS 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+cA-cA-cA-oT 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+cA-cA-cB-cA 1 0.000 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c2-X ) -+cA-cA-cB-cB 1 0.000 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c2-X ) -+cA-cA-cB-hB 1 0.000 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c2-X ) -+cA-cA-cD-cD 1 0.3112 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cD-cD 1 -0.1233 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cD-cD 1 0.1149 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cD-cD 1 -0.2199 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cD-cD 1 0.2170 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cD-hL 1 0.16 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(GAFF c3-c3-c3-hc) -+cA-cA-nA-cA 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X ) -+cA-cA-nA-hN 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X ) -+cA-cA-oH-hO 1 0.16 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-oh-ho) -+cA-cA-oH-hO 1 0.25 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-oh-ho) -+cA-cA-oS-cC 1 0.383 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-os-c ) -+cA-cA-oS-cC 1 0.80 180.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-os-c ) -+cA-cA-oT-pA 1 0.3833 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-os-X ) -+cA-cB-cA-hA 1 0.000 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c2-X ) -+cA-cB-cB-cA 1 6.65 180.0 -2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c2-c2-c3) -+cA-cB-cB-cA 1 1.90 180.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c2-c2-c3) -+cA-cB-cB-hB 1 6.650 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c2-c2-X ) -+cA-cD-cD-cD 1 0.3112 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cD-cD-cD 1 -0.1233 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cD-cD-cD 1 0.1149 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cD-cD-cD 1 -0.2199 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cD-cD-cD 1 0.2170 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cD-cD-hL 1 0.16 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(GAFF c3-c3-c3-hc) -+cA-nA-cA-hX 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X ) -+cA-oS-cC-cD 1 2.700 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -os-c -X ) -+cA-oS-cC-oC 1 2.70 180.0 -2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-c -o ) -+cA-oS-cC-oC 1 1.40 180.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-c -o ) -+cA-oS-cC-oS 1 2.700 180.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c -os-X ) -+cA-oT-pA-oP 1 0.800 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -os-p5-X ) -+cA-oT-pA-oT 1 0.25 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-p5-os) -+cA-oT-pA-oT 1 1.20 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-p5-os) -+cB-cA-cA-hA 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+cB-cA-cA-hE 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+cB-cA-cA-oH 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+cB-cB-cA-hA 1 0.38 180.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF hc-c3-c2-c2) -+cB-cB-cA-hA 1 1.15 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF hc-c3-c2-c2) -+cB-cB-cD-cD 1 0.3464 0.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cB-cD-cD 1 -0.5577 0.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cB-cD-cD 1 -0.2920 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cB-cD-cD 1 -0.0943 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cB-cD-cD 1 0.0226 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cB-cD-hL 1 0.38 180.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF c2-c2-c3-hc) -+cB-cB-cD-hL 1 1.15 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF c2-c2-c3-hc) -+cB-cD-cD-cD 1 0.0251 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cD-cD-cD 1 0.0054 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cD-cD-cD 1 0.2007 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cD-cD-cD 1 0.2103 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cD-cD-cD 1 0.0811 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cD-cD-hL 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c3-X ) -+cC-cD-cD-cD 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+cC-cD-cD-hL 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c3-X ) -+cC-oS-cA-hE 1 0.3833 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-os-X ) -+cD-cA-cA-hA 1 0.16 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(GAFF c3-c3-c3-hc) -+cD-cB-cB-cD 1 0.3073 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cB-cB-cD 1 4.0051 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cB-cB-cD 1 0.1990 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cB-cB-cD 1 0.3242 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cB-cB-cD 1 -0.0415 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cB-cB-hB 1 6.650 180.0 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c2-c2-X ) -+cD-cD-cA-hA 1 0.16 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(GAFF c3-c3-c3-hc) -+cD-cD-cB-hB 1 0.000 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c2-X ) -+cD-cD-cC-oC 1 -0.9110 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cC-oC 1 0.7382 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cC-oC 1 0.3290 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cC-oC 1 -0.5864 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cC-oC 1 0.1333 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cC-oS 1 -0.1226 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cC-oS 1 -0.2054 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cC-oS 1 0.1802 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cC-oS 1 0.5107 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cC-oS 1 0.1355 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cD-cD 1 0.3112 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cD-cD 1 -0.1233 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cD-cD 1 0.1149 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cD-cD 1 -0.2199 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cD-cD 1 0.2170 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cD-hL 1 0.16 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF c3-c3-c3-hc) -+hA-cA-cA-hA 1 0.15 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF hc-c3-c3-hc) -+hA-cA-cA-hE 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+hA-cA-cA-oH 1 0.00 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF hc-c3-c3-oh) -+hA-cA-cA-oH 1 0.25 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF hc-c3-c3-oh) -+hA-cA-cB-hB 1 0.000 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c2-X ) -+hA-cA-cD-hL 1 0.15 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(GAFF hc-c3-c3-hc) -+hB-cB-cB-hB 1 6.650 180.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c2-c2-X ) -+hB-cB-cD-hL 1 0.000 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c2-X ) -+hE-cA-cA-hE 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+hE-cA-cA-hX 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+hE-cA-cA-nA 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+hE-cA-cA-oS 1 0.00 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os) -+hE-cA-cA-oS 1 0.25 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os) -+hE-cA-cA-oT 1 0.00 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os) -+hE-cA-cA-oT 1 0.25 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os) -+hE-cA-oH-hO 1 0.500 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-oh-X ) -+hE-cA-oT-pA 1 0.3833 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-os-X ) -+hL-cD-cC-oC 1 0.08 180.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c -o ) -+hL-cD-cC-oC 1 0.80 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c -o ) -+hL-cD-cC-oS 1 0.000 180.0 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c -c3-X ) -+hL-cD-cD-hL 1 0.15 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c3-hc) -+hN-nA-cA-hX 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X ) -+hX-cA-cA-oT 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+nA-cA-cA-oT 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+oS-cA-cA-oS 1 0.144 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os) -+oS-cA-cA-oS 1 1.175 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os) -+oS-cA-cA-oT 1 0.144 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os) -+oS-cA-cA-oT 1 1.175 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os) -+ -+cA-cB-cB-cA 1.1 180. 2.0 Lipid14 CHL (GAFF) -+cB-cA-cB-hB 1.1 180. 2.0 Lipid14 CHL (GAFF) -+cB-cD-cB-hB 1.1 180.0 2.0 Lipid14 v2.0 aliphatic improper (GAFF c2-c3-c2-ha) - cD-oC-cC-oS 10.5 180.0 2.0 Lipid14 v2.0 ester improper (GAFF X -X -c -o ) --cB-cD-cB-hB 1.1 180.0 2.0 Lipid14 v2.0 aliphatic improper (GAFF c2-c3-c2-ha - default) - - hw ow 0000. 0000. 4. flag for fast water - Hack for no 10-12 terms - -@@ -156,17 +225,20 @@ MOD4 RE - cB 1.9080 0.0860 Lipid14 v2.10 - cC 1.9080 0.0700 Lipid14 v2.10 - cD 1.9080 0.1094 OPLS -+ hA 1.4870 0.0157 OPLS -+ hB 1.2500 0.0070 Lipid14 v2.10 -+ hE 1.3870 0.0157 Veenstra et al JCC,8,(1992),963 -+ hL 1.4600 0.0100 Lipid14 v2.10 -+ hN 0.6000 0.0157 !Ferguson base pair geom. -+ hO 0.0000 0.0000 OPLS Jorgensen, JACS,110,(1988),1657 (RCW Needs fixing give radii) -+ hX 1.1000 0.0157 Veenstra et al JCC,8,(1992),963 -+ nA 1.8240 0.1700 OPLS - oC 1.6500 0.1400 Lipid14 v2.10 -+ oH 1.7210 0.2104 OPLS -+ oP 1.6500 0.1400 Lipid14 v2.10 - oS 1.6500 0.1200 Lipid14 v2.10 - oT 1.6500 0.1200 Lipid14 v2.10 -- oP 1.6500 0.1400 Lipid14 v2.10 -- nA 1.8240 0.1700 OPLS - pA 2.1000 0.2000 JCC,7,(1986),230; -- hE 1.3870 0.0157 Veenstra et al JCC,8,(1992),963 -- hX 1.1000 0.0157 Veenstra et al JCC,8,(1992),963 -- hB 1.2500 0.0070 Lipid14 v2.10 -- hN 0.6000 0.0157 !Ferguson base pair geom. -- hL 1.4600 0.0100 Lipid14 v2.10 - - END - -@@ -175,7 +247,7 @@ END - - *** AMBER Lipid14 Force Field, C. Dickson, B. Madej, A.Skjevik, K. Teigen, I.R. Gould, R.C. Walker *** - --Citation is - Released version 2.10: -+Citation is: - - Dickson, C.J., Madej, B.D., Skjevik, A.A., Betz, R.M., Teigen, K., Gould, I.R., Walker, R.C., "Lipid14: The Amber Lipid Force Field", J. Chem. Theory Comput., 2014, in press, DOI: 10.1021/ct4010307 - -@@ -241,24 +313,31 @@ Version 2.11 (February 2014) - Version 2.12 (February 2014) - - Replace angle force constants involving phosporus with the correct values from the update GAFF.dat file. - -+Version 2.14 (September 2015) -+- Reorder parameters so they are alphabetical. -+- Add cholesterol parameters -+ - Atom type mapping - ----------------- - - GAFF Lipid14 Description - ---- ------- ----------- -- c3 cA sp3 carbon -- c2 cB aliphatic sp2 carbon - c cC carbonyl sp2 carbon -- o oC sp2 oxygen with one connected atom (e.g C=O, COO-) -- os oS sp3 oxygen in ethers and esters -- n4 nA sp3 N with four connected atoms -- p5 pA phosphorus with four connected atoms, such as O=P(OH)3 -+ c2 cB aliphatic sp2 carbon -+ c3 cA sp3 carbon - h1 hE H bonded to aliphatic carbon with 1 electrwd. group -- hx hX H bonded to C next to positively charged group - ha hB H bonded to aromatic carbon -+ hc hA H bonded to aliphatic carbon without electrwd. group - hn hN H bonded to nitrogen -+ ho hO H in Hydroxyl group -+ hx hX H bonded to C next to positively charged group -+ n4 nA sp3 N with four connected atoms -+ o oC sp2 oxygen with one connected atom (e.g C=O, COO-) - o oP sp2 oxygen with one connected atom (e.g P-O) in phosphate group -+ oh oH sp3 oxygen in hydroxyl group -+ os oS sp3 oxygen in ethers and esters - os oT sp3 oxygen bonded to carbon in phosphate group -+ p5 pA phosphorus with four connected atoms, such as O=P(OH)3 - - GAFFlipid Lipid14 Description - --------- ------- ----------- diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.5.patch b/sci-chemistry/ambertools/files/ambertools-15-update.5.patch deleted file mode 100644 index 017cb8d6d..000000000 --- a/sci-chemistry/ambertools/files/ambertools-15-update.5.patch +++ /dev/null @@ -1,25 +0,0 @@ -**********> update.5 - -Author: Jason Swails - -Date: Oct. 31, 2015 - -Program: ParmEd - -Description: Fix Python 2.6-compatibility for ParmEd - --------------------------------------------------------------------------------- - - AmberTools/src/parmed/chemistry/openmm/reporters.py | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git AmberTools/src/parmed/chemistry/openmm/reporters.py AmberTools/src/parmed/chemistry/openmm/reporters.py -index d4e47d4..0f4c3ea 100644 ---- AmberTools/src/parmed/chemistry/openmm/reporters.py -+++ AmberTools/src/parmed/chemistry/openmm/reporters.py -@@ -1,4 +1,4 @@ --from __future__ import division -+from __future__ import division, with_statement - - from chemistry.amber.asciicrd import AmberMdcrd - from chemistry.geometry import box_vectors_to_lengths_and_angles diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.6.patch b/sci-chemistry/ambertools/files/ambertools-15-update.6.patch deleted file mode 100644 index d7df551f5..000000000 --- a/sci-chemistry/ambertools/files/ambertools-15-update.6.patch +++ /dev/null @@ -1,59 +0,0 @@ -********> update.6 - -Author: Charles Lin - -Date: November 10, 2015 - -Programs: pmemd.cuda - -Description: This update gives support to cuda 7.5 and optional support for 7.0 (it is recommended to run cuda 6.5 or 7.5) - --------------------------------------------------------- - - AmberTools/src/configure2 | 31 ++++++++++++++++++++++++++++++- - 1 file changed, 30 insertions(+), 1 deletion(-) - -diff --git AmberTools/src/configure2 AmberTools/src/configure2 -index 9a504b1..6835c9c 100755 ---- AmberTools/src/configure2 -+++ AmberTools/src/configure2 -@@ -865,9 +865,38 @@ if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPXP" = 'yes' -o "$cuda_DPFP" = 'yes' ]; the - echo "CUDA Version $cudaversion detected" - echo "Configuring for SM2.0, SM3.0 and SM5.0" - nvccflags="$sm20flags $sm30flags $sm50flags" -+ elif [ "$cudaversion" = "7.0" ]; then -+ printf "\n" -+ printf "Version 7.0 of the NVIDIA CUDA compiler has been detected.\n\ -+Support for version 7.0 has been deprecated and we recommend use\n\ -+of either 7.5 or 6.5 instead. Version 7.0 introduced a performance\n\ -+regression over earlier compilers and also a bug in the way that GPUs are\n\ -+selected based on whether they are in use or not. This bug causes AMBER to\n\ -+print a GPU selection error rather than auto selecting a free GPU. These\n\ -+issues do not effect v6.5 and have been addressed in version 7.5." -+ printf "\n" -+ printf "If you still want to proceed with v7.0 on the\n\ -+understanding that it is considered deprecated from a support process please type\n\ -+'yes' to proceed. Otherwise type 'no', switch to either 6.5 or 7.5\n\ -+and rerun configure." -+ printf "\n" -+ read answer -+ ans=`echo $answer | awk '{print substr($1,1,1)}'` -+ -+ if [ "$ans" = "y" -o "$ans" = "Y" ]; then -+ echo "Configuring for SM2.0, SM3.0 and SM5.0" -+ nvccflags="$sm20flags $sm30flags $sm50flags" -+ else -+ echo "Please set cuda version to 6.5 or 7.5!" -+ exit 1 -+ fi -+ elif [ "$cudaversion" = "7.5" ]; then -+ echo "CUDA Version $cudaversion detected" -+ echo "Configuring for SM2.0, SM3.0, SM5.0 and SM5.2" -+ nvccflags="$sm20flags $sm30flags $sm50flags $sm52flags" - else - echo "Error: Unsupported CUDA version $cudaversion detected." -- echo " AMBER requires CUDA version == 5.0 .or. 5.5 .or. 6.0 .or. 6.5 .or. 7.0" -+ echo " AMBER requires CUDA version == 5.0 .or. 5.5 .or. 6.0 .or. 6.5 .or. 7.5" - exit 1 - fi - nvcc="$nvcc $nvccflags" diff --git a/sci-chemistry/ambertools/metadata.xml b/sci-chemistry/ambertools/metadata.xml deleted file mode 100644 index 7daa2ce7e..000000000 --- a/sci-chemistry/ambertools/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>alexxy@gentoo.org</email> - <name>Alexey Shvetsov</name> - </maintainer> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> |