proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

4 files changed, 541 insertions, 0 deletions

diff --git a/sci-chemistry/ambertools/Manifest b/sci-chemistry/ambertools/Manifest
new file mode 100644
index 000000000000..747dbffa95d4
--- /dev/null
+++ b/sci-chemistry/ambertools/Manifest
@@ -0,0 +1,2 @@
+DIST AmberTools-1.5.tar.bz2 121062582 SHA256 0c7d397d2e91603bb9123ae68e91af3525269e60800ced360f68c13350651d7c
+DIST ambertools-1.5-bugfix_1-10.patch.xz 31708 SHA256 5773aaa8a2478ad478f0f3afafaa39669002c31ebe755c0d12ff277ce9ab8352
diff --git a/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild
new file mode 100644
index 000000000000..47adf6201db7
--- /dev/null
+++ b/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild
@@ -0,0 +1,144 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils fortran-2 multilib toolchain-funcs
+
+DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
+HOMEPAGE="http://ambermd.org/#AmberTools"
+SRC_URI="
+	AmberTools-${PV}.tar.bz2
+	mirror://gentoo/${P}-bugfix_1-10.patch.xz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+IUSE="mpi openmp static-libs 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:2.1
+	sci-chemistry/reduce"
+DEPEND="${RDEPEND}
+	dev-util/byacc
+	dev-libs/libf2c
+	sys-devel/ucpp
+	virtual/pkgconfig"
+S="${WORKDIR}/amber11"
+
+pkg_nofetch() {
+	einfo "Go to ${HOMEPAGE} and get ${A}"
+	einfo "Place it in ${DISTDIR}"
+}
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	if use openmp; then
+		tc-has-openmp || \
+			die "Please select an openmp capable compiler like gcc[openmp]"
+	fi
+	AMBERHOME="${S}"
+}
+
+src_prepare() {
+	epatch \
+		"${WORKDIR}/${P}-bugfix_1-10.patch" \
+		"${FILESDIR}/${P}-gentoo.patch"
+	cd AmberTools/src
+	rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die
+}
+
+src_configure() {
+	cd AmberTools/src
+	sed \
+		-e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
+		-e "s:\\\\\$(LIBDIR)/lapack.a:$($(tc-getPKG_CONFIG) --libs lapack) -lclapack:g" \
+		-e "s:\\\\\$(LIBDIR)/blas.a:$($(tc-getPKG_CONFIG) --libs blas cblas):g" \
+		-e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
+		-e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
+		-e "s:CFLAGS=:CFLAGS=${CFLAGS} -DBINTRAJ :g" \
+		-e "s:FFLAGS=:FFLAGS=${FFLAGS} :g" \
+		-e "s:LDFLAGS=$ldflags:LDFLAGS=${LDFLAGS}:g" \
+		-e "s:fc=g77:fc=$(tc-getFC):g" \
+		-e "s:\$netcdflib:$($(tc-getPKG_CONFIG) --libs netcdf):g" \
+		-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
+		-e "s:-O3::g" \
+		-i configure || die
+	sed -e "s:arsecond_:arscnd_:g" \
+		-i sff/time.c \
+		-i sff/sff.h \
+		-i sff/sff.c || die
+	sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \
+		-i nss/Makefile || die
+
+	local myconf
+
+	use X || myconf="${myconf} -noX11"
+
+	for x in mpi openmp; do
+		use ${x} && myconf="${myconf} -${x}"
+	done
+
+	./configure \
+		${myconf} \
+		-nobintraj \
+		-nomdgx \
+		-nopython \
+		-nomtkpp \
+		gnu
+#	$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
+}
+
+src_compile() {
+	cd AmberTools/src
+	emake
+}
+
+src_install() {
+	rm -r bin/chemistry bin/MMPBSA_mods
+	rm bin/ante-MMPBSA.py bin/extractFrcmod.py
+	for x in bin/*
+		do dobin ${x} || die
+	done
+	rm "${ED}/usr/bin/yacc"
+	dobin AmberTools/src/antechamber/mopac.sh
+	sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \
+		-i "${ED}/usr/bin/mopac.sh" || die
+	# Make symlinks untill binpath for amber will be fixed
+	dodir /usr/share/${PN}/bin
+	cd "${ED}/usr/bin"
+	for x in *; do
+		dosym /usr/bin/${x} /usr/share/${PN}/bin/${x}
+	done
+	cd "${S}"
+#	sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \
+#		-i "${ED}/usr/bin/xleap" \
+#		-i "${ED}/usr/bin/tleap" || die
+	dodoc doc/AmberTools.pdf doc/leap_pg.pdf
+
+	use static-libs && dolib.a lib/*
+
+	insinto /usr/include/${PN}
+	doins include/*
+
+	insinto /usr/share/${PN}
+	doins -r dat
+
+	cd AmberTools
+	doins -r benchmarks examples test
+
+	cat >> "${T}"/99ambertools <<- EOF
+	AMBERHOME="${EPREFIX}/usr/share/ambertools"
+	EOF
+	doenvd "${T}"/99ambertools
+}
diff --git a/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch
new file mode 100644
index 000000000000..0e41d26d6f9c
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch
@@ -0,0 +1,386 @@
+diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/configure
+--- amber11.orig/AmberTools/src/configure	2011-04-14 15:30:55.000000000 +0300
++++ amber11/AmberTools/src/configure	2011-06-04 12:26:45.000000000 +0300
+@@ -293,7 +293,8 @@
+    echo "Your AMBERHOME environment variable is not set! It should be set to"
+    echo "$ambhome  NOT doing so may cause errors when you compile. Continue"
+    echo "anyway? (yes or no)"
+-   read answer
++   #read answer
++   answer='yes'
+    if [ "$answer" = 'yes' -o "$answer" = 'Yes' -o "$answer" = 'YES' -o "$answer" = 'y' -o "$answer" = 'Y' ]; then
+       echo ""
+       echo "Continuing anyway... Setting AMBERHOME to $ambhome temporarily"
+@@ -356,11 +357,11 @@
+ mpi_flag=
+ lex=flex
+ flibs_mkl=
+-lapack=install
+-blas=install
++lapack=skip
++blas=skip
+ f2c=skip
+-ucpp=install
+-cpp="\$(BINDIR)/ucpp -l"
++ucpp=skip
++cpp="\$(EPREFIX)/usr/bin/ucpp -l"
+ 
+ #-----------------------------------
+ # skip building of sleap?
+@@ -1655,24 +1656,24 @@
+   #--------------------------------------------------------------------------
+   #  Configure fftw-3.2.2:
+   #--------------------------------------------------------------------------
+-  if [ "$mdgx" = 'yes' ]; then
+-      mdgxflag="--prefix=$AMBERHOME --disable-fortran" 
+-      echo
+-      echo "Configuring fftw-3.2.2 (may be time-consuming)..."
+-      echo
+-      cd fftw-3.2.2 && \
+-      env CC="$cc" CFLAGS="$cflags $cnooptflags" \
+-          ./configure $mdgxflag > ../fftw3_config.log 2>&1
+-      ncerror=$?
+-      if [ $ncerror -gt 0 ]; then
+-          echo "    Error: FFTW configure returned $ncerror"
+-          echo "    FFTW configure failed! Check the fftw3_config.log file."
+-          exit 1
+-      else
+-          echo "    fftw-3.2.2 configure succeeded."
+-      fi
+-      cd ..
+-  fi
++  #if [ "$mdgx" = 'yes' ]; then
++  #    mdgxflag="--prefix=$AMBERHOME --disable-fortran" 
++  #    echo
++  #    echo "Configuring fftw-3.2.2 (may be time-consuming)..."
++  #    echo
++  #    cd fftw-3.2.2 && \
++  #    env CC="$cc" CFLAGS="$cflags $cnooptflags" \
++  #        ./configure $mdgxflag > ../fftw3_config.log 2>&1
++  #    ncerror=$?
++  #    if [ $ncerror -gt 0 ]; then
++  #        echo "    Error: FFTW configure returned $ncerror"
++  #        echo "    FFTW configure failed! Check the fftw3_config.log file."
++  #        exit 1
++  #    else
++  #        echo "    fftw-3.2.2 configure succeeded."
++  #    fi
++  #    cd ..
++  #fi
+ 
+   #--------------------------------------------------------------------------
+   #  Configure python
+@@ -1792,27 +1793,27 @@
+           echo
+           echo "Configuring fftw-2.1.5 (may be time-consuming)..."
+           echo
+-          cd fftw-2.1.5
+-          if [ "$mpi" = 'yes' ]; then
+-              ./configure $rismflag --enable-mpi \
+-              CC="$cc" CFLAGS="$cflags $coptflags" \
+-              F77="$fc" FFLAGS="$fflags $foptflags" \
+-                  FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1
+-          else
+-              ./configure $rismflag \
+-              CC="$cc" CFLAGS="$cflags $coptflags" \
+-              F77="$fc" FFLAGS="$fflags $foptflags" \
+-                  FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1
+-          fi
+-          ncerror=$?
+-          if [ $ncerror -gt 0 ]; then
+-              echo "    Error: fftw configure returned $ncerror"
+-              echo "    fftw configure failed!  Check the fftw2_config.log file."
+-              exit 1
+-          else
+-              echo "    fftw-2.1.5 configure succeeded."
+-          fi
+-          cd ..
++  #        cd fftw-2.1.5
++  #        if [ "$mpi" = 'yes' ]; then
++  #            ./configure $rismflag --enable-mpi \
++  #            CC="$cc" CFLAGS="$cflags $coptflags" \
++  #            F77="$fc" FFLAGS="$fflags $foptflags" \
++  #                FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1
++  #        else
++  #            ./configure $rismflag \
++  #            CC="$cc" CFLAGS="$cflags $coptflags" \
++  #            F77="$fc" FFLAGS="$fflags $foptflags" \
++  #                FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1
++  #        fi
++  #        ncerror=$?
++  #        if [ $ncerror -gt 0 ]; then
++  #            echo "    Error: fftw configure returned $ncerror"
++  #            echo "    fftw configure failed!  Check the fftw2_config.log file."
++  #            exit 1
++  #        else
++  #            echo "    fftw-2.1.5 configure succeeded."
++  #        fi
++  #        cd ..
+           flibs_fftw2="-ldrfftw -ldfftw"
+           if [ "$mpi" = 'yes' ]; then
+               flibs_fftw2="-ldrfftw_mpi -ldfftw_mpi $flibs_fftw2"
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/Makefile_at amber11/AmberTools/src/cpptraj/src/Makefile_at
+--- amber11.orig/AmberTools/src/cpptraj/src/Makefile_at	2011-04-14 15:30:16.000000000 +0300
++++ amber11/AmberTools/src/cpptraj/src/Makefile_at	2011-05-20 00:45:48.000000000 +0300
+@@ -65,8 +65,8 @@
+ 	-/bin/rm FindDepend.o
+ 	-/bin/rm findDepend
+ 
+-cpptraj$(SFX): $(NETCDFLIB) $(OBJECTS)
+-	$(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB)
++cpptraj$(SFX): $(OBJECTS)
++	$(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB) -lgomp
+ 
+ $(NETCDFLIB): ../../netcdf_config.log
+ 	cd ../../netcdf/src && $(MAKE) install
+diff -urN amber11.orig/AmberTools/src/Makefile amber11/AmberTools/src/Makefile
+--- amber11.orig/AmberTools/src/Makefile	2011-04-14 15:30:12.000000000 +0300
++++ amber11/AmberTools/src/Makefile	2011-05-19 23:36:36.000000000 +0300
+@@ -8,15 +8,15 @@
+ 
+ install: $(INSTALLTYPE)
+ 
+-serial: configured_serial $(NETCDFLIB) $(PYINSTALL) $(MTKPP)
++serial: configured_serial
+ 	@echo "Starting installation of ${AMBERTOOLS} serial at `date`".
+ #	utility routines and libraries:
+-	(cd ucpp-1.3 && $(MAKE) $(UCPP) )
++#	(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 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 )
+@@ -32,7 +32,7 @@
+ 	(cd cpptraj && $(MAKE) $(CPPTRAJ))
+ 
+ #   miscellaneous:
+-	(cd reduce && $(MAKE) install )
++#	(cd reduce && $(MAKE) install )
+ 
+ #   leap and gleap:
+ 	(cd leap && $(MAKE) install )
+@@ -42,7 +42,7 @@
+ 	(cd rism && $(MAKE) install )
+ 
+ #   nab:
+-	(cd cifparse && $(MAKE) install )
++#	(cd cifparse && $(MAKE) install )
+ 	(cd sff && $(MAKE) install )
+ 	(cd pbsa && $(MAKE) libinstall )
+ 	(cd nab && $(MAKE) install )
+@@ -63,19 +63,19 @@
+ 	@echo "Installation of ${AMBERTOOLS} serial is complete at `date`."
+ 	@echo ""
+ 
+-nabonly: $(NETCDFLIB) 
++nabonly:
+ #	utility routines and libraries:
+-	(cd ucpp-1.3 && $(MAKE) $(UCPP) )
++#	(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 arpack && $(MAKE) install );
++#	(cd lapack && $(MAKE) $(LAPACK) )
++#	(cd blas && $(MAKE) $(BLAS) )
++#	(cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
+ 	(cd pbsa && $(MAKE) libinstall )
+ 	(cd rism && $(MAKE) install )
+ 
+ #	nab:
+-	(cd cifparse && $(MAKE) install )
++#	(cd cifparse && $(MAKE) install )
+ 	(cd sff && $(MAKE) install )
+ 	(cd nab && $(MAKE) install )
+ 	(cd nss && $(MAKE) install )
+diff -urN amber11.orig/AmberTools/src/mdgx/Makefile amber11/AmberTools/src/mdgx/Makefile
+--- amber11.orig/AmberTools/src/mdgx/Makefile	2011-04-14 15:30:17.000000000 +0300
++++ amber11/AmberTools/src/mdgx/Makefile	2011-05-20 12:44:38.000000000 +0300
+@@ -109,7 +109,7 @@
+ 
+ FFTW_LIBS = $(LIBDIR)/libfftw3.a
+ 
+-mdgx$(SFX) : $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB)
++mdgx$(SFX) : $(MDGX_OBJS)
+ 	$(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \
+ 	-o $@ $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB) $(LM)
+ 
+diff -urN amber11.orig/AmberTools/src/pbsa/Makefile amber11/AmberTools/src/pbsa/Makefile
+--- amber11.orig/AmberTools/src/pbsa/Makefile	2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/pbsa/Makefile	2011-05-19 22:27:40.000000000 +0300
+@@ -148,7 +148,7 @@
+ 	)
+ 
+ #---------------------------------------------------------------------------
+-pbsa$(SFX): $(OBJ) syslib netlib c9x-complex configured_serial
++pbsa$(SFX): $(OBJ) syslib configured_serial
+ 	$(FC) $(FFLAGS) $(AMBERFFLAGS) -o pbsa$(SFX) $(OBJ) \
+ 	        ../lib/nxtsec.o ../lib/random.o \
+ 	        $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
+@@ -158,7 +158,7 @@
+ 	        ../lib/nxtsec.o ../lib/random.o \
+ 	        $(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) $(FFLAGS) $(AMBERFFLAGS) -o simplepbsa$(SFX) simplepbsa.o gopt.o \
+ 		libpbsa.a $(LIBDIR)/libsff.a ../lib/nxtsec.o $(FLIBSF) \
+ 		$(LDFLAGS) $(AMBERLDFLAGS)
+@@ -194,15 +194,15 @@
+ 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
++#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
+ 
+ %.LIBPBSA.o: %.f
+ 	$(FPP) $(FPPFLAGS) $(AMBERFPPFLAGS) -DLIBPBSA $< > _$<
+diff -urN amber11.orig/AmberTools/src/ptraj/Makefile amber11/AmberTools/src/ptraj/Makefile
+--- amber11.orig/AmberTools/src/ptraj/Makefile	2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/ptraj/Makefile	2011-05-19 23:38:36.000000000 +0300
+@@ -57,25 +57,25 @@
+ pubfft.o:  pubfft.f
+ 	$(FC) -c $(FREEFORMAT_FLAG) $(FOPTFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $<
+ 
+-rdparm$(SFX): libs $(NETCDFLIB) $(OBJECTS)
++rdparm$(SFX): libs $(OBJECTS)
+ 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
+ 		-o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
+ 
+-ptraj$(SFX): libs netlib $(NETCDFLIB) $(OBJECTS)
++ptraj$(SFX): libs $(OBJECTS)
+ 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
+ 		-o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
+ 
+-ptraj.MPI$(SFX): libs netlib $(PNETCDFLIB) $(OBJECTS)
++ptraj.MPI$(SFX): libs $(PNETCDFLIB) $(OBJECTS)
+ 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
+ 		-o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $(LM)
+ 
+ libs: 
+ 	cd pdb && $(MAKE) 
+-	cd ../arpack && $(MAKE)
++#	cd ../arpack && $(MAKE)
+ 
+-netlib:
+-	cd ../lapack && $(MAKE) $(LAPACK)
+-	cd ../blas && $(MAKE) $(BLAS)
++#netlib:
++#	cd ../lapack && $(MAKE) $(LAPACK)
++#	cd ../blas && $(MAKE) $(BLAS)
+ 
+ clean:
+ 	cd pdb && $(MAKE) clean
+diff -urN amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h amber11/AmberTools/src/ptraj/netcdf_ptraj.h
+--- amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h	2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/ptraj/netcdf_ptraj.h	2011-05-19 22:30:43.000000000 +0300
+@@ -4,7 +4,7 @@
+ #    include "../../include/pnetcdf.h"
+ #    define nc_strerror ncmpi_strerror
+ #  else
+-#    include "../../include/netcdf.h"
++#    include <netcdf.h>
+ #  endif 
+ #endif
+ 
+diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.h amber11/AmberTools/src/ptraj/ptraj.h
+--- amber11.orig/AmberTools/src/ptraj/ptraj.h	2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/ptraj/ptraj.h	2011-06-04 13:25:01.000000000 +0300
+@@ -94,7 +94,7 @@
+ #define nc_strerror ncmpi_strerror
+ #include "../../include/pnetcdf.h"
+ #else
+-#include "../../include/netcdf.h"
++#include <netcdf.h>
+ #endif
+ #endif
+ 
+diff -urN amber11.orig/AmberTools/src/rism/Makefile amber11/AmberTools/src/rism/Makefile
+--- amber11.orig/AmberTools/src/rism/Makefile	2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/rism/Makefile	2011-05-20 01:07:26.000000000 +0300
+@@ -49,7 +49,7 @@
+ 	mdiis_orig_c.o mdiis_blas_c.o mdiis_blas2_c.o mdiis_c.o \
+ 	fce_c.o erfcfun.o safemem.o blend.o timer_c.o
+ 
+-librism: $(LIBOBJ) $(FLIBS_FFTW2)
++librism: $(LIBOBJ)
+ 	$(AR) $(LIBDIR)/$@.a $(LIBOBJ)
+ 	$(RANLIB) $(LIBDIR)/$@.a
+ 
+diff -urN amber11.orig/AmberTools/src/sff/AmberNetcdf.c amber11/AmberTools/src/sff/AmberNetcdf.c
+--- amber11.orig/AmberTools/src/sff/AmberNetcdf.c	2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/sff/AmberNetcdf.c	2011-05-20 10:49:06.000000000 +0300
+@@ -27,7 +27,7 @@
+ #endif
+     
+ #ifdef BINTRAJ
+-#include "../../include/netcdf.h"
++#include <netcdf.h>
+ 
+ #define NCFRAME "frame"
+ #define NCSPATIAL "spatial"
+diff -urN amber11.orig/AmberTools/src/sff/Makefile amber11/AmberTools/src/sff/Makefile
+--- amber11.orig/AmberTools/src/sff/Makefile	2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/sff/Makefile	2011-05-20 09:53:27.000000000 +0300
+@@ -1,7 +1,7 @@
+ include ../config.h
+ 
+ .c.o:
+-	$(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) -o $@ $<
++	$(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) $(NETCDFLIB) -o $@ $<
+ 
+ OBJS = binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o nmode.o \
+ 	prm.o rand2.o sasad.o sff.o time.o xminC.o AmberNetcdf.o \
+diff -urN amber11.orig/AmberTools/src/sqm/Makefile amber11/AmberTools/src/sqm/Makefile
+--- amber11.orig/AmberTools/src/sqm/Makefile	2011-04-14 15:30:20.000000000 +0300
++++ amber11/AmberTools/src/sqm/Makefile	2011-05-19 22:31:49.000000000 +0300
+@@ -77,7 +77,7 @@
+ install: sqm$(SFX)
+ 	mv sqm$(SFX) $(BINDIR)
+ 
+-sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys
++sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys
+ 	$(FC) $(FFLAGS) $(AMBERFFLAGS) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) \
+ 		$(FLIBSF) ../lib/sys.a $(LDFLAGS) $(AMBERLDFLAGS)
+ 
+@@ -94,10 +94,10 @@
+ sys:
+ 	cd ../lib; $(MAKE) sys.a
+ 
+-netlib:
+-	cd ../lapack; $(MAKE) $(LAPACK)
+-	cd ../blas; $(MAKE) $(BLAS)
+-	cd ../arpack && $(MAKE) install
++#netlib:
++#	cd ../lapack; $(MAKE) $(LAPACK)
++#	cd ../blas; $(MAKE) $(BLAS)
++#	cd ../arpack && $(MAKE) install
+ 
+ clean:
+ 	/bin/rm -f *.o _*.f *.mod *.d sqm$(SFX)
diff --git a/sci-chemistry/ambertools/metadata.xml b/sci-chemistry/ambertools/metadata.xml
new file mode 100644
index 000000000000..13ef0bf5a17c
--- /dev/null
+++ b/sci-chemistry/ambertools/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>alexxy@gentoo.org</email>
+    <name>Alexey Shvetsov</name>
+  </maintainer>
+</pkgmetadata>