diff options
Diffstat (limited to 'sci-chemistry/gromacs/gromacs-9999.ebuild')
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-9999.ebuild | 52 |
1 files changed, 2 insertions, 50 deletions
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index 3a4fc186a..1ac609d8c 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -15,13 +15,12 @@ inherit autotools bash-completion eutils fortran git multilib toolchain-funcs DESCRIPTION="The ultimate molecular dynamics simulation package" HOMEPAGE="http://www.gromacs.org/" SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz ) - doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf ) - ffamber? ( http://ffamber.cnsm.csulb.edu/ffamber_v4.0-doc.tar.gz )" + doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )" LICENSE="GPL-2" SLOT="0" KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux" -IUSE="X blas dmalloc doc -double-precision ffamber +fftw fkernels +gsl lapack +IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack mpi +single-precision static static-libs test +threads +xml zsh-completion" DEPEND="app-shells/tcsh @@ -233,53 +232,6 @@ src_install() { cd "${S}" dodoc AUTHORS INSTALL README 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() { |