[sci-chemistry/ambertools] Moved to tree =D

8 files changed, 0 insertions, 1159 deletions

diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog
deleted file mode 100644
index d51fa1a46..000000000
--- a/sci-chemistry/ambertools/ChangeLog
+++ /dev/null
@@ -1,29 +0,0 @@
-# ChangeLog for sci-chemistry/ambertools
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-  24 Jun 2011; Justin Lecher <jlec@gentoo.org> ambertools-1.4.ebuild,
-  -files/ambertools-1.4-bugfix_1-18.patch, ambertools-1.5.ebuild,
-  -files/ambertools-1.5-bugfix_1-3.patch:
-  Cleaned ebuild
-
-  23 Jun 2011; Justin Lecher <jlec@gentoo.org> ambertools-1.4.ebuild,
-  ambertools-1.5.ebuild:
-  Streamlined fortran-2 eclass usage
-
-  21 Jun 2011; Justin Lecher <jlec@gentoo.org> ambertools-1.4.ebuild,
-  ambertools-1.5.ebuild:
-  Added fortran-2.eclass support
-
-*ambertools-1.5 (04 Jun 2011)
-
-  04 Jun 2011; Reinis Danne <rei4dan@gmail.com> +ambertools-1.5.ebuild,
-  +files/ambertools-1.5-bugfix_1-3.patch, +files/ambertools-1.5-gentoo.patch:
-  Version bump.
-
-  15 Mar 2011; Justin Lecher <jlec@gentoo.org> ambertools-1.4.ebuild:
-  Remove fortran.eclass
-
-  14 Mar 2011; Justin Lecher <jlec@gentoo.org> ambertools-1.4.ebuild:
-  Remove fortran.eclass removal
-
diff --git a/sci-chemistry/ambertools/Manifest b/sci-chemistry/ambertools/Manifest
deleted file mode 100644
index 4c54ae5a9..000000000
--- a/sci-chemistry/ambertools/Manifest
+++ /dev/null
@@ -1,32 +0,0 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
-
-AUX ambertools-1.4-gentoo.patch 9926 RMD160 d84b121e1fa940cbf949855de3a5f0bee7566330 SHA1 08ea41b969bed5320230420d047e71a28333f76c SHA256 8f520c01146a704173ca31c68dc9440e2938263416f6d0c95de22d138426e01f
-AUX ambertools-1.5-gentoo.patch 14083 RMD160 762c52626c4eda51839caf74c001bb660052706a SHA1 ab0afa1f5b73569539515dba4cf6638a594c7d6e SHA256 82a83f660701c192272e79f5bab17a8a8be945d78fdab454ade3918281749922
-DIST AmberTools-1.4.tar.bz2 67331137 RMD160 b499e18b583a0b454dd3a554986c19c111822e6a SHA1 ef0f9a44c8767ed35f942fd41afc636b67da0389 SHA256 af61da2f3643b4ec7f41620242b734a3cb4a79c5d422100fbd1fd1c402fecfc1
-DIST AmberTools-1.5.tar.bz2 121062582 RMD160 4a086b42c378f0904f7bf0b16adb042f1677be55 SHA1 92e47e7337fb4901a5a145d808c5ffd42c82d08d SHA256 0c7d397d2e91603bb9123ae68e91af3525269e60800ced360f68c13350651d7c
-DIST ambertools-1.4-bugfix_1-18.patch.xz 48136 RMD160 83fe98ef2f4620cd4c85fc72147f830ddfa47b51 SHA1 7a5a2cba9172d017d83aed16ece06d6fed6a5196 SHA256 7ea936442ce1b29943e867adaeb69932d297ae50e0a63b0e03cfb18953e9f7c2
-DIST ambertools-1.5-bugfix_1-10.patch.xz 31708 RMD160 6366e6cae9084a2de96102fc75049bc982a23bfa SHA1 248f088131e8f0efa6d61ae3afbff64571551032 SHA256 5773aaa8a2478ad478f0f3afafaa39669002c31ebe755c0d12ff277ce9ab8352
-DIST ambertools-1.5-bugfix_1-3.patch.xz 27268 RMD160 18a74e2e84e81d39417f656ef93e8ee4d4d4583d SHA1 bc52c0776d151a8db005bb7bfb40bf9e963bdeba SHA256 edec6ccc275ee0a70b2ecc9316c031249c4f32d89b1aa145cee32c862516049a
-EBUILD ambertools-1.4.ebuild 3201 RMD160 b2f4331166bafc5093f04c4e7ad9bf2eee9ee0e5 SHA1 4033d6225f7e86d42292eed5ddecd7edeb6742ec SHA256 e3a77f1a006832c46117a5c6a6a641685965f8dfe0c949c0ec1e2f7e57f73835
-EBUILD ambertools-1.5-r1.ebuild 3338 RMD160 f8d6560c30243ae569ff743bb4b6d03e9af2546c SHA1 b210b4895c8151db217d1f7c080de325a6fabc2d SHA256 312409b7ac9581163ceeb4541d3097ce1beb5bc594ef7a4b741e29878e59b0a7
-EBUILD ambertools-1.5.ebuild 3336 RMD160 d97fc7eade8bcf0d12596d42a512560671751d18 SHA1 0427a45349e95be91e274d0e12eb2eb484da6dd3 SHA256 8f8f33770cb12253fef10e9b651a567de36a2863d674b82ca3b1959ab8684353
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diff --git a/sci-chemistry/ambertools/ambertools-1.4.ebuild b/sci-chemistry/ambertools/ambertools-1.4.ebuild
deleted file mode 100644
index 5e75cdb63..000000000
--- a/sci-chemistry/ambertools/ambertools-1.4.ebuild
+++ /dev/null
@@ -1,133 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-inherit eutils fortran-2 toolchain-funcs
-
-DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
-HOMEPAGE="http://ambermd.org/#AmberTools"
-SRC_URI="
-	AmberTools-${PV}.tar.bz2
-	mirror://gentoo/${P}-bugfix_1-18.patch.xz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="mpi openmp X"
-
-RESTRICT="fetch"
-
-RDEPEND="
-	virtual/cblas
-	virtual/lapack
-	sci-libs/arpack
-	sci-libs/cifparse-obj
-	sci-chemistry/mopac7
-	sci-libs/netcdf
-	sci-chemistry/reduce
-	virtual/fortran"
-DEPEND="${RDEPEND}
-	dev-util/byacc
-	dev-libs/libf2c
-	sys-devel/ucpp"
-S="${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_1-18.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:$(pkg-config lapack --libs) -lclapack:g" \
-		-e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):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=$(tc-getFC):g" \
-		-e "s:NETCDFLIB=\$netcdflib:NETCDFLIB=$(pkg-config netcdf --libs):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 \
-		gnu
-#	$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
-}
-
-src_compile() {
-	cd AmberTools/src
-	emake || die
-}
-
-src_install() {
-	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 "${ED}/usr/bin/tleap" || die
-	dodoc doc/AmberTools.pdf doc/leap_pg.pdf
-	dolib.a lib/*
-	insinto /usr/include/${PN}
-	doins include/*
-	insinto /usr/share/${PN}
-	doins -r dat
-	cd AmberTools
-	doins -r benchmarks
-	doins -r examples
-	doins -r test
-	cat >> "${T}"/99ambertools <<- EOF
-	AMBERHOME="${EPREFIX}/usr/share/ambertools"
-	EOF
-	doenvd "${T}"/99ambertools
-}
diff --git a/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild
deleted file mode 100644
index da44cf5ef..000000000
--- a/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild
+++ /dev/null
@@ -1,140 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-inherit eutils fortran-2 toolchain-funcs
-
-DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
-HOMEPAGE="http://ambermd.org/#AmberTools"
-SRC_URI="
-	AmberTools-${PV}.tar.bz2
-	mirror://gentoo/${P}-bugfix_1-10.patch.xz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="mpi 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:2.1
-	sci-chemistry/reduce
-	virtual/fortran"
-DEPEND="${RDEPEND}
-	dev-util/byacc
-	dev-libs/libf2c
-	sys-devel/ucpp"
-S="${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:$(pkg-config lapack --libs) -lclapack:g" \
-		-e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):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=$(tc-getFC):g" \
-		-e "s:\$netcdflib:$(pkg-config netcdf --libs):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 || die
-}
-
-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 "${ED}/usr/bin/tleap" || die
-	dodoc doc/AmberTools.pdf doc/leap_pg.pdf
-	dolib.a lib/*
-	insinto /usr/include/${PN}
-	doins include/*
-	insinto /usr/share/${PN}
-	doins -r dat
-	cd AmberTools
-	doins -r benchmarks
-	doins -r examples
-	doins -r test
-	cat >> "${T}"/99ambertools <<- EOF
-	AMBERHOME="${EPREFIX}/usr/share/ambertools"
-	EOF
-	doenvd "${T}"/99ambertools
-}
diff --git a/sci-chemistry/ambertools/ambertools-1.5.ebuild b/sci-chemistry/ambertools/ambertools-1.5.ebuild
deleted file mode 100644
index 9ac9755e7..000000000
--- a/sci-chemistry/ambertools/ambertools-1.5.ebuild
+++ /dev/null
@@ -1,140 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-inherit eutils fortran-2 toolchain-funcs
-
-DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
-HOMEPAGE="http://ambermd.org/#AmberTools"
-SRC_URI="
-	AmberTools-${PV}.tar.bz2
-	mirror://gentoo/${P}-bugfix_1-3.patch.xz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="mpi 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:2.1
-	sci-chemistry/reduce
-	virtual/fortran"
-DEPEND="${RDEPEND}
-	dev-util/byacc
-	dev-libs/libf2c
-	sys-devel/ucpp"
-S="${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_1-3.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:$(pkg-config lapack --libs) -lclapack:g" \
-		-e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):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=$(tc-getFC):g" \
-		-e "s:\$netcdflib:$(pkg-config netcdf --libs):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 || die
-}
-
-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 "${ED}/usr/bin/tleap" || die
-	dodoc doc/AmberTools.pdf doc/leap_pg.pdf
-	dolib.a lib/*
-	insinto /usr/include/${PN}
-	doins include/*
-	insinto /usr/share/${PN}
-	doins -r dat
-	cd AmberTools
-	doins -r benchmarks
-	doins -r examples
-	doins -r test
-	cat >> "${T}"/99ambertools <<- EOF
-	AMBERHOME="${EPREFIX}/usr/share/ambertools"
-	EOF
-	doenvd "${T}"/99ambertools
-}
diff --git a/sci-chemistry/ambertools/files/ambertools-1.4-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-1.4-gentoo.patch
deleted file mode 100644
index c067928cb..000000000
--- a/sci-chemistry/ambertools/files/ambertools-1.4-gentoo.patch
+++ /dev/null
@@ -1,289 +0,0 @@
-diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/configure
---- amber11.orig/AmberTools/src/configure	2010-04-23 18:17:17.000000000 +0400
-+++ amber11/AmberTools/src/configure	2011-03-07 03:39:14.000000000 +0300
-@@ -288,11 +288,11 @@
- 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?
-@@ -1241,24 +1241,24 @@
-   #--------------------------------------------------------------------------
-   #  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" ./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" ./configure $mdgxflag \
-+  #            > ../fftw3_config.log 2>&1
-+  #    ncerror=$?
-+  #    if [ $ncerror -gt 0 ]; then
-+  #        echo "    Error: fftw configure returned $ncerror"
-+  #        echo "    fftw configure failed!  Check the fftw3_config.log file."
-+  #        exit 1
-+  #    else
-+  #        echo "    fftw-3.2.2 configure succeeded."
-+  #    fi
-+  #    cd ..
-+  #fi
- 
-   #--------------------------------------------------------------------------
-   #  Set up MPI 3D-RISM in NAB and SANDER
-@@ -1307,23 +1307,23 @@
-           echo
-           echo "Configuring fftw-2.1.5; (may be time-consuming)"
-           echo
--          cd fftw-2.1.5
--          if [ "$mpi" = 'yes' ]; then
--              ./configure $rismflag --enable-mpi CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \
--                  > ../fftw2_config.log 2>&1
--          else
--              ./configure $rismflag CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \
--                  > ../fftw2_config.log 2>&1
--          fi
--          ncerror=$?
--          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="$cflags" F77="$fc" FFLAGS="$fflags" \
-+ #                 > ../fftw2_config.log 2>&1
-+ #         else
-+ #             ./configure $rismflag CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \
-+ #                 > ../fftw2_config.log 2>&1
-+ #         fi
-+ #         ncerror=$?
-+ #         if [ $ncerror -gt 0 ]; then
-+ #             echo "    Error: fftw configure returned $ncerror"
-+ #             echo "    fftw configure failed!  Check the fftw2_config.log file."
-+ #             exit 1
-+ #         else
-+ #             echo "    fftw-2.1.5 configure succeeded."
-+ #         fi
-+ #         cd ..
-           flibs_fftw2="\$(LIBDIR)/libdrfftw.a \$(LIBDIR)/libdfftw.a"
-           if [ "$mpi" = 'yes' ]; then
-               flibs_fftw2="\$(LIBDIR)/libdrfftw_mpi.a \$(LIBDIR)/libdfftw_mpi.a $flibs_fftw2"
-diff -urN amber11.orig/AmberTools/src/Makefile amber11/AmberTools/src/Makefile
---- amber11.orig/AmberTools/src/Makefile	2010-04-14 17:36:31.000000000 +0400
-+++ amber11/AmberTools/src/Makefile	2011-03-07 03:39:38.000000000 +0300
-@@ -8,15 +8,15 @@
- 
- install: serial
- 
--serial: configured_serial $(NETCDFLIB)
-+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 )
-@@ -30,14 +30,14 @@
- 	(cd ptraj && $(MAKE) install )
- 
- #   miscellaneous:
--	(cd reduce && $(MAKE) install )
-+#	(cd reduce && $(MAKE) install )
- 
- #   leap and gleap:
- 	(cd leap && $(MAKE) install )
- 	(cd gleap && $(MAKE) install )
- 
- #	nab:
--	(cd cifparse && $(MAKE) install )
-+#	(cd cifparse && $(MAKE) install )
- 	(cd nab && $(MAKE) install )
- 	(cd nss && $(MAKE) install )
- 
-@@ -50,15 +50,15 @@
- 
- nabonly: $(NETCDFLIB) 
- #	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) )
- 
- #	nab:
--	(cd cifparse && $(MAKE) install )
-+#	(cd cifparse && $(MAKE) install )
- 	(cd nab && $(MAKE) install )
- 	(cd nss && $(MAKE) install )
- 
-diff -urN amber11.orig/AmberTools/src/pbsa/Makefile amber11/AmberTools/src/pbsa/Makefile
---- amber11.orig/AmberTools/src/pbsa/Makefile	2010-04-14 17:26:17.000000000 +0400
-+++ amber11/AmberTools/src/pbsa/Makefile	2011-03-07 03:39:15.000000000 +0300
-@@ -47,10 +47,10 @@
- 	$(LIBDIR)/libpbsa.a $(LIBDIR)/libFpbsa.a
- 
- #---------------------------------------------------------------------------
--pbsa$(SFX): $(OBJ) syslib netlib c9x-complex
-+pbsa$(SFX): $(OBJ) syslib
- 	$(FC) -o pbsa$(SFX) $(OBJ) ../lib/nxtsec.o $(FLIBSF) $(LDFLAGS)
- 
--simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9x-complex
-+simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib
- 	$(FC) -o simplepbsa$(SFX) simplepbsa.o gopt.o libpbsa.a \
- 	$(LIBDIR)/libsff.a ../lib/nxtsec.o $(FLIBSF) $(LDFLAGS)
- 	/bin/mv simplepbsa$(SFX) $(BINDIR)
-@@ -76,15 +76,15 @@
- 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) -DLIBPBSA $< > _$<
-diff -urN amber11.orig/AmberTools/src/ptraj/Makefile amber11/AmberTools/src/ptraj/Makefile
---- amber11.orig/AmberTools/src/ptraj/Makefile	2010-03-31 07:05:16.000000000 +0400
-+++ amber11/AmberTools/src/ptraj/Makefile	2011-03-07 03:39:16.000000000 +0300
-@@ -60,20 +60,20 @@
- rdparm$(SFX): libs $(NETCDFLIB) $(OBJECTS)
- 	$(CC) $(LDFLAGS) -o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
- 
--ptraj$(SFX): libs netlib $(NETCDFLIB) $(OBJECTS)
-+ptraj$(SFX): libs $(NETCDFLIB) $(OBJECTS)
- 	$(CC) $(LDFLAGS) -o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
- 
--ptraj.MPI$(SFX): libs netlib $(PNETCDFLIB) $(OBJECTS)
-+ptraj.MPI$(SFX): libs $(PNETCDFLIB) $(OBJECTS)
- 	$(CC) $(LDFLAGS) -o ptraj.MPI$(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; $(MAKE) clean
-diff -urN amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h amber11/AmberTools/src/ptraj/netcdf_ptraj.h
---- amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h	2010-03-31 07:05:16.000000000 +0400
-+++ amber11/AmberTools/src/ptraj/netcdf_ptraj.h	2011-03-07 03:39:17.000000000 +0300
-@@ -4,7 +4,7 @@
- #    include "../pnetcdf/include/pnetcdf.h"
- #    define nc_strerror ncmpi_strerror
- #  else
--#    include "../netcdf/include/netcdf.h"
-+#    include <netcdf.h>
- #  endif 
- #endif
- 
-diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.h amber11/AmberTools/src/ptraj/ptraj.h
---- amber11.orig/AmberTools/src/ptraj/ptraj.h	2010-03-31 07:05:16.000000000 +0400
-+++ amber11/AmberTools/src/ptraj/ptraj.h	2011-03-07 03:39:17.000000000 +0300
-@@ -94,7 +94,7 @@
- #define nc_strerror ncmpi_strerror
- #include "../pnetcdf/include/pnetcdf.h"
- #else
--#include "../netcdf/include/netcdf.h"
-+#include <netcdf.h>
- #endif
- #endif
- 
-diff -urN amber11.orig/AmberTools/src/sqm/Makefile amber11/AmberTools/src/sqm/Makefile
---- amber11.orig/AmberTools/src/sqm/Makefile	2010-04-14 16:13:28.000000000 +0400
-+++ amber11/AmberTools/src/sqm/Makefile	2011-03-07 03:39:17.000000000 +0300
-@@ -77,7 +77,7 @@
- install: sqm$(SFX)
- 	mv sqm$(SFX) $(BINDIR)
- 
--sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys
-+sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys
- 	$(FC) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) $(FLIBSF) ../lib/sys.a $(LDFLAGS)
- 
- #-----------LIBS
-@@ -93,10 +93,10 @@
- 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/files/ambertools-1.5-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch
deleted file mode 100644
index 0e41d26d6..000000000
--- a/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch
+++ /dev/null
@@ -1,386 +0,0 @@
-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
deleted file mode 100644
index 20e218e23..000000000
--- a/sci-chemistry/ambertools/metadata.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?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>
-