[sci-chemistry/gromacs] Update ebuild to eapi3+prefix support. add amberports and latest upstream patches

(Portage version: 2.2_rc67_p177/cvs/Linux x86_64)

6 files changed, 91 insertions, 340 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index b383a4bcf902..f24ceea63123 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,15 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.50 2010/06/24 13:08:43 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.51 2010/06/27 19:06:33 alexxy Exp $
+
+*gromacs-4.0.7-r3 (27 Jun 2010)
+
+  27 Jun 2010; Alexey Shvetsov <alexxy@gentoo.org> -gromacs-4.0.7.ebuild,
+  -gromacs-4.0.7-r1.ebuild, +gromacs-4.0.7-r3.ebuild,
+  -files/gromacs-4.0.7-docdir.patch,
+  +files/gromacs-4.0.7_upstream2010-06-08.patch:
+  Added patches from upstream stable branch. Added ffamber ports. Also fixed
+  bugs #301854 and #284431. Big thank to Christoph Junghans
 
   24 Jun 2010; Justin Lecher <jlec@gentoo.org> gromacs-3.3.1-r1.ebuild,
   gromacs-3.3.3.ebuild:
diff --git a/sci-chemistry/gromacs/files/gromacs-4.0.7-docdir.patch b/sci-chemistry/gromacs/files/gromacs-4.0.7-docdir.patch
deleted file mode 100644
index b556947b9c2c..000000000000
--- a/sci-chemistry/gromacs/files/gromacs-4.0.7-docdir.patch
+++ /dev/null
@@ -1,72 +0,0 @@
-diff -Naur gromacs-4.0.5.orig/share/html/Makefile.am gromacs-4.0.5/share/html/Makefile.am
---- gromacs-4.0.5.orig/share/html/Makefile.am	2006-03-06 10:52:20.000000000 +0100
-+++ gromacs-4.0.5/share/html/Makefile.am	2009-11-29 22:27:24.000000000 +0100
-@@ -4,7 +4,7 @@
- #
- SUBDIRS = .  images  online
- 
--htmldir = ${pkgdatadir}/html
-+htmldir = @htmldir@/html
- 
- html_DATA = online.html gmxfaq.html
- 
-diff -Naur gromacs-4.0.5.orig/share/html/Makefile.in gromacs-4.0.5/share/html/Makefile.in
---- gromacs-4.0.5.orig/share/html/Makefile.in	2009-05-09 11:12:24.000000000 +0200
-+++ gromacs-4.0.5/share/html/Makefile.in	2009-11-29 22:28:16.000000000 +0100
-@@ -172,7 +172,7 @@
- host_cpu = @host_cpu@
- host_os = @host_os@
- host_vendor = @host_vendor@
--htmldir = ${pkgdatadir}/html
-+htmldir = @htmldir@/html
- includedir = @includedir@
- infodir = @infodir@
- install_sh = @install_sh@
-diff -Naur gromacs-4.0.5.orig/share/html/images/Makefile.am gromacs-4.0.5/share/html/images/Makefile.am
---- gromacs-4.0.5.orig/share/html/images/Makefile.am	2006-03-06 10:52:20.000000000 +0100
-+++ gromacs-4.0.5/share/html/images/Makefile.am	2009-11-29 23:00:57.000000000 +0100
-@@ -2,7 +2,7 @@
- #
- # Don't edit - this file is generated automatically from Makefile.am
- #
--imagedir = ${pkgdatadir}/html/images
-+imagedir = @htmldir@/html/images
- 
- image_DATA = \
- 	features.gif					\
-diff -Naur gromacs-4.0.5.orig/share/html/images/Makefile.in gromacs-4.0.5/share/html/images/Makefile.in
---- gromacs-4.0.5.orig/share/html/images/Makefile.in	2009-05-09 11:12:24.000000000 +0200
-+++ gromacs-4.0.5/share/html/images/Makefile.in	2009-11-29 23:01:20.000000000 +0100
-@@ -186,7 +186,7 @@
- #
- # Don't edit - this file is generated automatically from Makefile.am
- #
--imagedir = ${pkgdatadir}/html/images
-+imagedir = @htmldir@/html/images
- image_DATA = \
- 	features.gif					\
- 	flow_leftrightup.gif	flow_vrule.gif 		\
-diff -Naur gromacs-4.0.5.orig/share/html/online/Makefile.am gromacs-4.0.5/share/html/online/Makefile.am
---- gromacs-4.0.5.orig/share/html/online/Makefile.am	2008-08-11 11:46:17.000000000 +0200
-+++ gromacs-4.0.5/share/html/online/Makefile.am	2009-11-29 23:01:47.000000000 +0100
-@@ -2,7 +2,7 @@
- #
- # Don't edit - this file is generated automatically from Makefile.am
- #
--onlinedir = ${pkgdatadir}/html/online
-+onlinedir = @htmldir@/html/online
- 
- online_DATA = \
-   cpt.html	\
-diff -Naur gromacs-4.0.5.orig/share/html/online/Makefile.in gromacs-4.0.5/share/html/online/Makefile.in
---- gromacs-4.0.5.orig/share/html/online/Makefile.in	2009-05-09 11:12:24.000000000 +0200
-+++ gromacs-4.0.5/share/html/online/Makefile.in	2009-11-29 23:02:15.000000000 +0100
-@@ -186,7 +186,7 @@
- #
- # Don't edit - this file is generated automatically from Makefile.am
- #
--onlinedir = ${pkgdatadir}/html/online
-+onlinedir = @htmldir@/html/online
- online_DATA = \
-   cpt.html	\
-   dat.html           g_disre.html      g_sorient.html        ndx.html        \
diff --git a/sci-chemistry/gromacs/files/gromacs-4.0.7_upstream2010-06-08.patch.gz b/sci-chemistry/gromacs/files/gromacs-4.0.7_upstream2010-06-08.patch.gz
new file mode 100644
index 000000000000..41dcc8702ccd
--- /dev/null
+++ b/sci-chemistry/gromacs/files/gromacs-4.0.7_upstream2010-06-08.patch.gz
diff --git a/sci-chemistry/gromacs/gromacs-4.0.7-r1.ebuild b/sci-chemistry/gromacs/gromacs-4.0.7-r3.ebuild
index abc141e621b4..bb224ca48383 100644
--- a/sci-chemistry/gromacs/gromacs-4.0.7-r1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.0.7-r3.ebuild
@@ -1,8 +1,8 @@
 # Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.7-r1.ebuild,v 1.1 2010/01/24 19:39:09 alexxy Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.7-r3.ebuild,v 1.1 2010/06/27 19:06:33 alexxy Exp $
 
-EAPI="2"
+EAPI="3"
 
 LIBTOOLIZE="true"
 TEST_PV="4.0.4"
@@ -13,12 +13,14 @@ DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
 SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
 		test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )"
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )
+		ffamber? ( http://ffamber.cnsm.csulb.edu/ffamber_v4.0-doc.tar.gz )"
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
-IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack mpi +single-precision static test +xml zsh-completion"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
+IUSE="X blas dmalloc doc -double-precision ffamber +fftw fkernels +gsl lapack
+mpi +single-precision static static-libs test +xml zsh-completion"
 
 DEPEND="app-shells/tcsh
 	X? ( x11-libs/libX11
@@ -38,6 +40,9 @@ RESTRICT="test"
 
 src_prepare() {
 
+	epatch "${FILESDIR}/${P}_upstream2010-06-08.patch.gz"
+	sed -e '/AC_INIT/s/4\.0\.7/&-2010-06-08/' -i configure.ac \
+		|| die "Failed to change version in configure.ac"
 	epatch "${FILESDIR}/${PN}-4.0.9999-docdir.patch"
 	epatch "${FILESDIR}/${PN}-4.0.9999-ccache.patch"
 	# Fix typos in a couple of files.
@@ -45,7 +50,7 @@ src_prepare() {
 		|| die "Failed to fixup demo script."
 
 	# Fix a sandbox violation that occurs when re-emerging with mpi.
-	sed "/libdir=\"\$(libdir)\"/ a\	temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
+	sed "/libdir=\"\$(libdir)\"/ a\	temp_libdir=\"${ED}usr/$( get_libdir )\" ; \\\\" \
 	-i src/tools/Makefile.am \
 	|| die "sed tools/Makefile.am failed"
 
@@ -53,7 +58,7 @@ src_prepare() {
 	-i src/tools/Makefile.am \
 	|| die "sed tools/Makefile.am failed"
 
-	sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
+	sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${ED}usr/$( get_libdir )\" ; \\\\" \
 	-i src/tools/Makefile.am \
 	|| die "sed tools/Makefile.am failed"
 
@@ -125,15 +130,16 @@ src_configure() {
 
 	# by default its better to have dynamicaly linked binaries
 	if use static; then
+		#gmx build static libs by default
 		myconf="${myconf} $(use_enable static all-static)"
 	else
-		myconf="${myconf} --enable-shared"
+		myconf="${myconf} --enable-shared $(use_enable static-libs static)"
 	fi
 
-	myconf="--datadir=/usr/share \
-			--bindir=/usr/bin \
-			--libdir=/usr/$(get_libdir) \
-			--docdir=/usr/share/doc/"${PF}" \
+	myconf="--datadir="${EPREFIX}"/usr/share \
+			--bindir="${EPREFIX}"/usr/bin \
+			--libdir="${EPREFIX}"/usr/$(get_libdir) \
+			--docdir="${EPREFIX}"/usr/share/doc/"${PF}" \
 			$(use_with dmalloc) \
 			$(use_with fftw fft fftw3) \
 			$(use_with gsl) \
@@ -206,26 +212,74 @@ src_test() {
 src_install() {
 	for x in ${GMX_DIRS}; do
 		cd "${S}-${x}"
-		emake DESTDIR="${D}" install || die "emake install for ${x} failed"
+		emake DESTDIR="${ED}" install || die "emake install for ${x} failed"
 		use mpi || continue
 		cd "${S}-${x}_mpi"
-		emake DESTDIR="${D}" install-mdrun || die "emake install-mdrun for ${x} failed"
+		emake DESTDIR="${ED}" install-mdrun || die "emake install-mdrun for ${x} failed"
 	done
 
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${D}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
+	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
 	doenvd "${T}/80gromacs"
-	rm -f "${D}"/usr/bin/GMXRC*
+	rm -f "${ED}"/usr/bin/GMXRC*
 
-	dobashcompletion "${D}"/usr/bin/completion.bash ${PN}
+	dobashcompletion "${ED}"/usr/bin/completion.bash ${PN}
 	if use zsh-completion ; then
 		insinto /usr/share/zsh/site-functions
-		newins "${D}"/usr/bin/completion.zsh _${PN}
+		newins "${ED}"/usr/bin/completion.zsh _${PN}
 	fi
-	rm -r "${D}"/usr/bin/completion.*
+	rm -r "${ED}"/usr/bin/completion.*
 
 	cd "${S}"
 	dodoc AUTHORS INSTALL README
-	use doc && dodoc "${DISTDIR}"/manual-4.0.pdf
+	use doc && dodoc "${DISTDIR}/manual-4.0.pdf"
+
+	if use ffamber; then
+		use doc && dodoc "${WORKDIR}/ffamber_v4.0/README/pdfs/*.pdf"
+		# prepare vdwradii.dat
+		cat >>"${ED}"/usr/share/gromacs/top/vdwradii.dat <<-EOF
+			SOL  MW    0
+			SOL  LP    0
+		EOF
+		# regenerate aminoacids.dat
+		cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \
+		"${ED}"/usr/share/gromacs/top/aminoacids.dat \
+		| awk '{print $1}' | sort -u | tail -n+4 | wc -l \
+		>> "${ED}"/usr/share/gromacs/top/aminoacids.dat.new
+		cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \
+		"${ED}"/usr/share/gromacs/top/aminoacids.dat \
+		| awk '{print $1}' | sort -u | tail -n+4 \
+		>> "${ED}"/usr/share/gromacs/top/aminoacids.dat.new
+		mv -f "${ED}"/usr/share/gromacs/top/aminoacids.dat.new \
+		"${ED}"/usr/share/gromacs/top/aminoacids.dat
+		# copy ff files
+		for x in ffamber94 ffamber96 ffamber99 ffamber99p ffamber99sb \
+				ffamberGS ffamberGSs ffamber03 ; do
+			einfo "Adding ${x} to gromacs"
+			cp "${WORKDIR}"/ffamber_v4.0/${x}/* "${ED}"/usr/share/gromacs/top
+		done
+		# copy suplementary files
+		cp "${WORKDIR}"/ffamber_v4.0/*.gro "${ED}"/usr/share/gromacs/top
+		cp "${WORKDIR}"/ffamber_v4.0/*.itp "${ED}"/usr/share/gromacs/top
+		# actualy add records to FF.dat
+		cat >>"${ED}"/usr/share/gromacs/top/FF.dat.new <<-EOF
+			ffamber94   AMBER94 Cornell protein/nucleic forcefield
+			ffamber96   AMBER96 Kollman protein/nucleic forcefield
+			ffamberGS   AMBER-GS Garcia &  Sanbonmatsu forcefield
+			ffamberGSs  AMBER-GSs Nymeyer &  Garcia forcefield
+			ffamber99   AMBER99 Wang protein/nucleic acid forcefield
+			ffamber99p  AMBER99p protein/nucleic forcefield
+			ffamber99sb AMBER99sb Hornak protein/nucleic forcefield
+			ffamber03   AMBER03 Duan protein/nucleic forcefield
+		EOF
+		cat "${ED}"/usr/share/gromacs/top/FF.dat \
+			"${ED}"/usr/share/gromacs/top/FF.dat.new \
+			| tail -n+2 > "${ED}"/usr/share/gromacs/top/FF.dat.new2
+		cat "${ED}"/usr/share/gromacs/top/FF.dat.new2 | wc -l > \
+			"${ED}"/usr/share/gromacs/top/FF.dat
+		cat "${ED}"/usr/share/gromacs/top/FF.dat.new2 >> \
+			"${ED}"/usr/share/gromacs/top/FF.dat
+		rm -f "${ED}"/usr/share/gromacs/top/FF.dat.new*
+	fi
 }
 
 pkg_postinst() {
diff --git a/sci-chemistry/gromacs/gromacs-4.0.7.ebuild b/sci-chemistry/gromacs/gromacs-4.0.7.ebuild
deleted file mode 100644
index 5b6f1bd4093d..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.0.7.ebuild
+++ /dev/null
@@ -1,242 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.7.ebuild,v 1.2 2009/12/08 15:08:23 alexxy Exp $
-
-EAPI="2"
-
-LIBTOOLIZE="true"
-TEST_PV="4.0.4"
-
-inherit autotools bash-completion eutils fortran multilib
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
-		test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
-IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack mpi +single-precision static test +xml zsh-completion"
-
-DEPEND="app-shells/tcsh
-	X? ( x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE )
-	dmalloc? ( dev-libs/dmalloc )
-	blas? ( virtual/blas )
-	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2 )"
-
-RDEPEND="${DEPEND}"
-
-RESTRICT="test"
-
-src_prepare() {
-
-	epatch "${FILESDIR}/${P}-docdir.patch"
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	# Fix a sandbox violation that occurs when re-emerging with mpi.
-	sed "/libdir=\"\$(libdir)\"/ a\	temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed -e "s:\$\$libdir:\$temp_libdir:" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed -e "s:\$\$libdir:\$\$temp_libdir:" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	use fkernels && epatch "${FILESDIR}/${PN}-4.0.4-configure-gfortran.patch"
-
-	eautoreconf
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" single"
-	use double-precision && GMX_DIRS+=" double"
-	for x in ${GMX_DIRS}; do
-		mkdir "${S}-${x}" || die
-		use test && cp -r "${WORKDIR}"/gmxtest "${S}-${x}"
-		use mpi || continue
-		mkdir "${S}-${x}_mpi" || die
-	done
-}
-
-src_configure() {
-	local myconf
-	local myconfsingle
-	local myconfdouble
-	local suffixdouble
-
-	#leave all assembly options enabled mdrun is smart enough to deside itself
-	#there so no gentoo on bluegene!
-	myconf="${myconf} --disable-bluegene"
-
-	#from gromacs configure
-	if ! use fftw; then
-		ewarn "WARNING: The built-in FFTPACK routines are slow."
-		ewarn "Are you sure you don\'t want to use FFTW?"
-		ewarn "It is free and much faster..."
-	fi
-
-	if [[ $(gcc-version) == "4.1" ]]; then
-		eerror "gcc 4.1 is not supported by gromacs"
-		eerror "please run test suite"
-		die
-	fi
-
-	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
-	#fortran will gone in gromacs 4.1 anyway
-	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
-	if use fkernels; then
-		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
-		ewarn "I hope, you know what are you doing..."
-		FORTRAN="g77 gfortran ifc"
-		myconf="${myconf} --enable-fortran" && fortran_pkg_setup
-	else
-		myconf="${myconf} --disable-fortran"
-	fi
-
-	# if we need external blas
-	if use blas; then
-		export LIBS="${LIBS} -lblas"
-		myconf="${myconf} $(use_with blas external-blas)"
-	fi
-
-	# if we need external lapack
-	if use lapack; then
-		export LIBS="${LIBS} -llapack"
-		myconf="${myconf} $(use_with lapack external-lapack)"
-	fi
-
-	# by default its better to have dynamicaly linked binaries
-	if use static; then
-		myconf="${myconf} $(use_enable static all-static)"
-	else
-		myconf="${myconf} --enable-shared"
-	fi
-
-	myconf="--datadir=/usr/share \
-			--bindir=/usr/bin \
-			--libdir=/usr/$(get_libdir) \
-			--docdir=/usr/share/doc/"${PF}" \
-			$(use_with dmalloc) \
-			$(use_with fftw fft fftw3) \
-			$(use_with gsl) \
-			$(use_with X x) \
-			$(use_with xml) \
-			${myconf}"
-
-	#if we build single and double - double is suffixed
-	if ( use double-precision && use single-precision ); then
-		suffixdouble="_d"
-	else
-		suffixdouble=""
-	fi
-
-	if use double-precision ; then
-		#from gromacs manual
-		elog
-		elog "For most simulations single precision is accurate enough. In some"
-		elog "cases double precision is required to get reasonable results:"
-		elog
-		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
-		elog " and the calculation and diagonalization of the Hessian "
-		elog "-calculation of the constraint force between two large groups of	atoms"
-		elog "-energy conservation: this can only be done without temperature coupling and"
-		elog " without cutoffs"
-		elog
-	fi
-
-	if use mpi ; then
-		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
-		elog "we configure/compile gromacs twice (with and without mpi) and only"
-		elog "install mdrun with mpi support. In addtion you will get libgmx and"
-		elog "libmd with and without mpi support."
-	fi
-
-	myconfdouble="${myconf} --enable-double --program-suffix='${suffixdouble}'"
-	myconfsingle="${myconf} --enable-float --program-suffix=''"
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		cd "${S}-${x}"
-		local p=myconf${x}
-		ECONF_SOURCE="${S}" econf ${!p} --disable-mpi
-		use mpi || continue
-		cd "${S}-${x}_mpi"
-		ECONF_SOURCE="${S}" econf ${!p} --enable-mpi
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		cd "${S}-${x}"
-		einfo "Compiling for ${x} precision"
-		emake || die "emake for ${x} precision failed"
-		use mpi || continue
-		cd "${S}-${x}_mpi"
-		emake mdrun || die "emake mdrun for ${x} precision failed"
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		local oldpath="${PATH}"
-		export PATH="${S}-${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
-		cd "${S}-${x}"
-		emake -j1 tests || die "${x} Precision test failed"
-		export PATH="${oldpath}"
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		cd "${S}-${x}"
-		emake DESTDIR="${D}" install || die "emake install for ${x} failed"
-		use mpi || continue
-		cd "${S}-${x}_mpi"
-		emake DESTDIR="${D}" install-mdrun || die "emake install-mdrun for ${x} failed"
-	done
-
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${D}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
-	doenvd "${T}/80gromacs"
-	rm -f "${D}"/usr/bin/GMXRC*
-
-	dobashcompletion "${D}"/usr/bin/completion.bash ${PN}
-	if use zsh-completion ; then
-		insinto /usr/share/zsh/site-functions
-		newins "${D}"/usr/bin/completion.zsh _${PN}
-	fi
-	rm -r "${D}"/usr/bin/completion.*
-
-	cd "${S}"
-	dodoc AUTHORS INSTALL README
-	use doc && dodoc "${DISTDIR}"/manual-4.0.pdf
-}
-
-pkg_postinst() {
-	env-update && source /etc/profile
-	elog
-	elog "Please read and cite:"
-	elog "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	elog "http://dx.doi.org/10.1021/ct700301q"
-	elog
-	bash-completion_pkg_postinst
-	elog
-	elog $(luck)
-	elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
-	elog
-}
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index bf268860cf37..c0e0dfc97a93 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -3,10 +3,12 @@
 <pkgmetadata>
 <herd>sci-chemistry</herd>
 <use>
-	<flag name='dmalloc'>Enable debugging with the dmalloc library</flag>
-	<flag name='double-precision'>More precise calculations at the expense of speed</flag>
-	<flag name='fkernels'>Enable building of Fortran Kernels for platforms that
-	dont have assembly loops</flag>
-	<flag name='single-precision'>Single precision version of gromacs</flag>
+  <flag name='dmalloc'>Enable use of Debug Malloc</flag>
+  <flag name='double-precision'>More precise calculations at the expense of speed</flag>
+  <flag name='ffamber'>Enable ffamber ports for gromacs</flag>
+  <flag name='fkernels'>Enable building of Fortran Kernels for platforms
+	  that dont have assembly loops</flag>
+  <flag name='single-precision'>Single precision version of gromacs</flag>
+  <flag name='zsh-completion'>Enable zsh completion support</flag>
 </use>
 </pkgmetadata>