10 files changed, 548 insertions, 267 deletions
diff --git a/biology/gromacs/Makefile b/biology/gromacs/Makefile
index c9646e837c2..3e9e8da5d55 100644
--- a/biology/gromacs/Makefile
+++ b/biology/gromacs/Makefile
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.3 2010/07/31 19:14:08 dholland Exp $
+# $NetBSD: Makefile,v 1.4 2010/09/03 20:52:39 asau Exp $
 #
 
-DISTNAME=		gromacs-4.0.7
-PKGREVISION=		2
+DISTNAME=		gromacs-4.5.1
 CATEGORIES=		biology
 MASTER_SITES=		ftp://ftp.gromacs.org/pub/gromacs/
 
@@ -18,10 +17,12 @@ PKG_DESTDIR_SUPPORT=	user-destdir
 GNU_CONFIGURE=		yes
 USE_LIBTOOL=		yes
 USE_PKGLOCALEDIR=	yes
+USE_TOOLS+=		pkg-config
 
 CONFIGURE_ARGS+=	--enable-shared
 CONFIGURE_ARGS+=	--enable-double --program-suffix=
 CONFIGURE_ARGS+=	--with-gsl
+CONFIGURE_ARGS+=	--disable-gcc41-check
 
 .include "options.mk"
 
diff --git a/biology/gromacs/PLIST b/biology/gromacs/PLIST
index 4fc7f1146ba..fd58b375648 100644
--- a/biology/gromacs/PLIST
+++ b/biology/gromacs/PLIST
@@ -1,9 +1,8 @@
-@comment $NetBSD: PLIST,v 1.2 2010/05/16 12:04:03 asau Exp $
+@comment $NetBSD: PLIST,v 1.3 2010/09/03 20:52:39 asau Exp $
 bin/GMXRC
 bin/GMXRC.bash
 bin/GMXRC.csh
 bin/GMXRC.zsh
-bin/anadock
 bin/completion.bash
 bin/completion.csh
 bin/completion.zsh
@@ -11,9 +10,11 @@ bin/demux.pl
 bin/do_dssp
 bin/editconf
 bin/eneconv
+bin/g_anadock
 bin/g_anaeig
 bin/g_analyze
 bin/g_angle
+bin/g_bar
 bin/g_bond
 bin/g_bundle
 bin/g_chi
@@ -38,9 +39,10 @@ bin/g_h2order
 bin/g_hbond
 bin/g_helix
 bin/g_helixorient
-bin/g_kinetics
 bin/g_lie
+bin/g_luck
 bin/g_mdmat
+bin/g_membed
 bin/g_mindist
 bin/g_morph
 bin/g_msd
@@ -48,28 +50,36 @@ bin/g_nmeig
 bin/g_nmens
 bin/g_nmtraj
 bin/g_order
+bin/g_pme_error
 bin/g_polystat
 bin/g_potential
 bin/g_principal
+bin/g_protonate
 bin/g_rama
 bin/g_rdf
 bin/g_rms
 bin/g_rmsdist
 bin/g_rmsf
 bin/g_rotacf
+bin/g_rotmat
 bin/g_saltbr
 bin/g_sas
-bin/g_sdf
+bin/g_select
 bin/g_sgangle
 bin/g_sham
+bin/g_sigeps
 bin/g_sorient
 bin/g_spatial
 bin/g_spol
 bin/g_tcaf
 bin/g_traj
+bin/g_tune_pme
 bin/g_vanhove
 bin/g_velacc
 bin/g_wham
+bin/g_wheel
+bin/g_x2top
+${PLIST.x11}bin/g_xrama
 bin/genbox
 bin/genconf
 bin/genion
@@ -77,25 +87,18 @@ bin/genrestr
 bin/gmxcheck
 bin/gmxdump
 bin/grompp
-${PLIST.x11}bin/highway
-bin/luck
 bin/make_edi
 bin/make_ndx
 bin/mdrun
 bin/mk_angndx
 ${PLIST.x11}bin/ngmx
 bin/pdb2gmx
-bin/protonate
-bin/sigeps
 bin/tpbconv
 bin/trjcat
 bin/trjconv
 bin/trjorder
-bin/wheel
-bin/x2top
 bin/xplor2gmx.pl
 bin/xpm2ps
-${PLIST.x11}bin/xrama
 include/gromacs/3dview.h
 include/gromacs/assert.h
 include/gromacs/atomprop.h
@@ -103,12 +106,15 @@ include/gromacs/bondf.h
 include/gromacs/calcgrid.h
 include/gromacs/calch.h
 include/gromacs/calcmu.h
+include/gromacs/centerofmass.h
+include/gromacs/chargegroup.h
 include/gromacs/checkpoint.h
 include/gromacs/confio.h
 include/gromacs/constr.h
 include/gromacs/copyrite.h
 include/gromacs/coulomb.h
 include/gromacs/dihre.h
+include/gromacs/displacement.h
 include/gromacs/disre.h
 include/gromacs/do_fit.h
 include/gromacs/domdec.h
@@ -117,45 +123,60 @@ include/gromacs/ebin.h
 include/gromacs/edsam.h
 include/gromacs/enxio.h
 include/gromacs/ffscanf.h
-include/gromacs/fftgrid.h
 include/gromacs/filenm.h
 include/gromacs/force.h
 include/gromacs/futil.h
 include/gromacs/gbutil.h
+include/gromacs/gen_ad.h
+include/gromacs/genborn.h
 include/gromacs/gmx_ana.h
 include/gromacs/gmx_arpack.h
 include/gromacs/gmx_blas.h
 include/gromacs/gmx_cyclecounter.h
 include/gromacs/gmx_fatal.h
 include/gromacs/gmx_fft.h
+include/gromacs/gmx_ga2la.h
 include/gromacs/gmx_lapack.h
+include/gromacs/gmx_matrix.h
 include/gromacs/gmx_parallel_3dfft.h
 include/gromacs/gmx_random.h
+include/gromacs/gmx_sort.h
+include/gromacs/gmx_sse2_double.h
+include/gromacs/gmx_sse2_single.h
+include/gromacs/gmx_statistics.h
 include/gromacs/gmx_system_xdr.h
-include/gromacs/gmx_thread.h
 include/gromacs/gmx_wallcycle.h
 include/gromacs/gmxcomplex.h
+include/gromacs/gmxcpp.h
 include/gromacs/gmxfio.h
 include/gromacs/gpp_atomtype.h
 include/gromacs/gpp_nextnb.h
 include/gromacs/grompp.h
 include/gromacs/gstat.h
+include/gromacs/hackblock.h
+include/gromacs/histogram.h
 include/gromacs/index.h
+include/gromacs/indexutil.h
+include/gromacs/inputrec.h
 include/gromacs/invblock.h
 include/gromacs/macros.h
 include/gromacs/magic.h
 include/gromacs/main.h
+include/gromacs/mainpage.h
 include/gromacs/maths.h
 include/gromacs/matio.h
+include/gromacs/md5.h
 include/gromacs/mdatoms.h
 include/gromacs/mdebin.h
 include/gromacs/mdrun.h
+include/gromacs/molfile_plugin.h
 include/gromacs/mpelogging.h
 include/gromacs/mshift.h
 include/gromacs/mtop_util.h
 include/gromacs/mtxio.h
 include/gromacs/mvdata.h
 include/gromacs/names.h
+include/gromacs/nbsearch.h
 include/gromacs/network.h
 include/gromacs/nonbonded.h
 include/gromacs/nrama.h
@@ -163,14 +184,17 @@ include/gromacs/nrjac.h
 include/gromacs/nrnb.h
 include/gromacs/ns.h
 include/gromacs/nsgrid.h
+include/gromacs/oenv.h
 include/gromacs/orires.h
 include/gromacs/partdec.h
 include/gromacs/pbc.h
+include/gromacs/pdb2top.h
 include/gromacs/pdbio.h
-include/gromacs/pdebug.h
 include/gromacs/perf_est.h
 include/gromacs/physics.h
 include/gromacs/pme.h
+include/gromacs/poscalc.h
+include/gromacs/position.h
 include/gromacs/pppm.h
 include/gromacs/princ.h
 include/gromacs/pull.h
@@ -178,29 +202,54 @@ include/gromacs/qmmm.h
 include/gromacs/random.h
 include/gromacs/rbin.h
 include/gromacs/rdgroup.h
-include/gromacs/readcomp.h
 include/gromacs/readinp.h
-include/gromacs/reorder.h
+include/gromacs/resall.h
 include/gromacs/rmpbc.h
+include/gromacs/selection.h
+include/gromacs/selmethod.h
+include/gromacs/selparam.h
+include/gromacs/selvalue.h
+include/gromacs/sfactor.h
 include/gromacs/shellfc.h
 include/gromacs/shift.h
+include/gromacs/sighandler.h
 include/gromacs/smalloc.h
 include/gromacs/sortwater.h
 include/gromacs/sparsematrix.h
 include/gromacs/split.h
 include/gromacs/splitter.h
-include/gromacs/statusio.h
 include/gromacs/statutil.h
 include/gromacs/strdb.h
 include/gromacs/string2.h
-include/gromacs/struc2.h
 include/gromacs/symtab.h
 include/gromacs/sysstuff.h
-include/gromacs/tags.h
 include/gromacs/tgroup.h
+include/gromacs/thread_mpi.h
+include/gromacs/thread_mpi/atomic.h
+include/gromacs/thread_mpi/atomic/gcc.h
+include/gromacs/thread_mpi/atomic/gcc_ia64.h
+include/gromacs/thread_mpi/atomic/gcc_intrinsics.h
+include/gromacs/thread_mpi/atomic/gcc_ppc.h
+include/gromacs/thread_mpi/atomic/gcc_spinlock.h
+include/gromacs/thread_mpi/atomic/gcc_x86.h
+include/gromacs/thread_mpi/atomic/hpux.h
+include/gromacs/thread_mpi/atomic/msvc.h
+include/gromacs/thread_mpi/atomic/xlc_ppc.h
+include/gromacs/thread_mpi/barrier.h
+include/gromacs/thread_mpi/collective.h
+include/gromacs/thread_mpi/event.h
+include/gromacs/thread_mpi/hwinfo.h
+include/gromacs/thread_mpi/list.h
+include/gromacs/thread_mpi/lock.h
+include/gromacs/thread_mpi/mpi_bindings.h
+include/gromacs/thread_mpi/threads.h
+include/gromacs/thread_mpi/tmpi.h
+include/gromacs/thread_mpi/wait.h
+include/gromacs/tmpi.h
 include/gromacs/topsort.h
+include/gromacs/toputil.h
 include/gromacs/tpxio.h
-include/gromacs/transfer.h
+include/gromacs/trajana.h
 include/gromacs/trnio.h
 include/gromacs/txtdump.h
 include/gromacs/typedefs.h
@@ -213,6 +262,7 @@ include/gromacs/types/enums.h
 include/gromacs/types/fcdata.h
 include/gromacs/types/filenm.h
 include/gromacs/types/forcerec.h
+include/gromacs/types/genborn.h
 include/gromacs/types/graph.h
 include/gromacs/types/group.h
 include/gromacs/types/idef.h
@@ -222,10 +272,10 @@ include/gromacs/types/ishift.h
 include/gromacs/types/matrix.h
 include/gromacs/types/mdatom.h
 include/gromacs/types/nblist.h
-include/gromacs/types/nbslist.h
 include/gromacs/types/nrnb.h
 include/gromacs/types/ns.h
 include/gromacs/types/nsgrid.h
+include/gromacs/types/oenv.h
 include/gromacs/types/pbc.h
 include/gromacs/types/qmmmrec.h
 include/gromacs/types/shellfc.h
@@ -235,11 +285,14 @@ include/gromacs/types/symtab.h
 include/gromacs/types/topology.h
 include/gromacs/types/trx.h
 include/gromacs/update.h
-include/gromacs/utils.h
 include/gromacs/vcm.h
 include/gromacs/vec.h
 include/gromacs/viewit.h
+include/gromacs/vmddlopen.h
+include/gromacs/vmdio.h
+include/gromacs/vmdplugin.h
 include/gromacs/vsite.h
+include/gromacs/warninp.h
 include/gromacs/wgms.h
 include/gromacs/wman.h
 include/gromacs/writeps.h
@@ -248,14 +301,20 @@ include/gromacs/xtcio.h
 include/gromacs/xvgr.h
 lib/libgmx${MPI}_d.la
 lib/libgmxana${MPI}_d.la
+lib/libgmxpreprocess${MPI}_d.la
 lib/libmd${MPI}_d.la
-man/man1/anadock.1
+lib/pkgconfig/libgmx${MPI}_d.pc
+lib/pkgconfig/libgmxana${MPI}_d.pc
+lib/pkgconfig/libgmxpreprocess${MPI}_d.pc
+lib/pkgconfig/libmd${MPI}_d.pc
 man/man1/do_dssp.1
 man/man1/editconf.1
 man/man1/eneconv.1
+man/man1/g_anadock.1
 man/man1/g_anaeig.1
 man/man1/g_analyze.1
 man/man1/g_angle.1
+man/man1/g_bar.1
 man/man1/g_bond.1
 man/man1/g_bundle.1
 man/man1/g_chi.1
@@ -280,9 +339,9 @@ man/man1/g_h2order.1
 man/man1/g_hbond.1
 man/man1/g_helix.1
 man/man1/g_helixorient.1
-man/man1/g_kinetics.1
 man/man1/g_lie.1
 man/man1/g_mdmat.1
+man/man1/g_membed.1
 man/man1/g_mindist.1
 man/man1/g_morph.1
 man/man1/g_msd.1
@@ -293,26 +352,32 @@ man/man1/g_order.1
 man/man1/g_polystat.1
 man/man1/g_potential.1
 man/man1/g_principal.1
+man/man1/g_protonate.1
 man/man1/g_rama.1
 man/man1/g_rdf.1
 man/man1/g_rms.1
 man/man1/g_rmsdist.1
 man/man1/g_rmsf.1
 man/man1/g_rotacf.1
+man/man1/g_rotmat.1
 man/man1/g_saltbr.1
 man/man1/g_sas.1
-man/man1/g_sdf.1
+man/man1/g_select.1
 man/man1/g_sgangle.1
 man/man1/g_sham.1
+man/man1/g_sigeps.1
 man/man1/g_sorient.1
 man/man1/g_spatial.1
 man/man1/g_spol.1
 man/man1/g_tcaf.1
 man/man1/g_traj.1
+man/man1/g_tune_pme.1
 man/man1/g_vanhove.1
 man/man1/g_velacc.1
 man/man1/g_wham.1
-man/man1/gen_table.1
+man/man1/g_wheel.1
+man/man1/g_x2top.1
+man/man1/g_xrama.1
 man/man1/genbox.1
 man/man1/genconf.1
 man/man1/genion.1
@@ -320,23 +385,18 @@ man/man1/genrestr.1
 man/man1/gmxcheck.1
 man/man1/gmxdump.1
 man/man1/grompp.1
-man/man1/highway.1
 man/man1/make_edi.1
 man/man1/make_ndx.1
 man/man1/mdrun.1
 man/man1/mk_angndx.1
 man/man1/ngmx.1
 man/man1/pdb2gmx.1
-man/man1/protonate.1
-man/man1/sigeps.1
 man/man1/tpbconv.1
 man/man1/trjcat.1
 man/man1/trjconv.1
 man/man1/trjorder.1
-man/man1/wheel.1
-man/man1/x2top.1
 man/man1/xpm2ps.1
-man/man1/xrama.1
+man/man7/gromacs.7
 share/gromacs/html/gmxfaq.html
 share/gromacs/html/images/1ctf-0.2.jpg
 share/gromacs/html/images/1ctf-0.5.jpg
@@ -493,142 +553,467 @@ share/gromacs/html/online/xtc.html
 share/gromacs/html/online/xvg.html
 share/gromacs/html/online/yourown.html
 share/gromacs/template/Makefile.${MACHINE_GNU_PLATFORM}_double
+share/gromacs/template/Makefile.pkg
 share/gromacs/template/README
 share/gromacs/template/template.c
-share/gromacs/top/1mlg.itp
-share/gromacs/top/2mlg.itp
-share/gromacs/top/FF.dat
-share/gromacs/top/aminoacids.dat
+share/gromacs/top/amber03.ff/aminoacids.arn
+share/gromacs/top/amber03.ff/aminoacids.c.tdb
+share/gromacs/top/amber03.ff/aminoacids.hdb
+share/gromacs/top/amber03.ff/aminoacids.n.tdb
+share/gromacs/top/amber03.ff/aminoacids.r2b
+share/gromacs/top/amber03.ff/aminoacids.rtp
+share/gromacs/top/amber03.ff/aminoacids.vsd
+share/gromacs/top/amber03.ff/atomtypes.atp
+share/gromacs/top/amber03.ff/dna.arn
+share/gromacs/top/amber03.ff/dna.hdb
+share/gromacs/top/amber03.ff/dna.r2b
+share/gromacs/top/amber03.ff/dna.rtp
+share/gromacs/top/amber03.ff/ffbonded.itp
+share/gromacs/top/amber03.ff/ffnonbonded.itp
+share/gromacs/top/amber03.ff/forcefield.doc
+share/gromacs/top/amber03.ff/forcefield.itp
+share/gromacs/top/amber03.ff/gbsa.itp
+share/gromacs/top/amber03.ff/ions.itp
+share/gromacs/top/amber03.ff/rna.arn
+share/gromacs/top/amber03.ff/rna.hdb
+share/gromacs/top/amber03.ff/rna.r2b
+share/gromacs/top/amber03.ff/rna.rtp
+share/gromacs/top/amber03.ff/spc.itp
+share/gromacs/top/amber03.ff/spce.itp
+share/gromacs/top/amber03.ff/tip3p.itp
+share/gromacs/top/amber03.ff/tip4p.itp
+share/gromacs/top/amber03.ff/tip4pew.itp
+share/gromacs/top/amber03.ff/tip5p.itp
+share/gromacs/top/amber03.ff/urea.itp
+share/gromacs/top/amber03.ff/watermodels.dat
+share/gromacs/top/amber94.ff/aminoacids.arn
+share/gromacs/top/amber94.ff/aminoacids.c.tdb
+share/gromacs/top/amber94.ff/aminoacids.hdb
+share/gromacs/top/amber94.ff/aminoacids.n.tdb
+share/gromacs/top/amber94.ff/aminoacids.r2b
+share/gromacs/top/amber94.ff/aminoacids.rtp
+share/gromacs/top/amber94.ff/aminoacids.vsd
+share/gromacs/top/amber94.ff/atomtypes.atp
+share/gromacs/top/amber94.ff/dna.arn
+share/gromacs/top/amber94.ff/dna.hdb
+share/gromacs/top/amber94.ff/dna.r2b
+share/gromacs/top/amber94.ff/dna.rtp
+share/gromacs/top/amber94.ff/ffbonded.itp
+share/gromacs/top/amber94.ff/ffnonbonded.itp
+share/gromacs/top/amber94.ff/forcefield.doc
+share/gromacs/top/amber94.ff/forcefield.itp
+share/gromacs/top/amber94.ff/gbsa.itp
+share/gromacs/top/amber94.ff/ions.itp
+share/gromacs/top/amber94.ff/rna.arn
+share/gromacs/top/amber94.ff/rna.hdb
+share/gromacs/top/amber94.ff/rna.r2b
+share/gromacs/top/amber94.ff/rna.rtp
+share/gromacs/top/amber94.ff/spc.itp
+share/gromacs/top/amber94.ff/spce.itp
+share/gromacs/top/amber94.ff/tip3p.itp
+share/gromacs/top/amber94.ff/tip4p.itp
+share/gromacs/top/amber94.ff/tip4pew.itp
+share/gromacs/top/amber94.ff/tip5p.itp
+share/gromacs/top/amber94.ff/urea.itp
+share/gromacs/top/amber94.ff/watermodels.dat
+share/gromacs/top/amber96.ff/aminoacids.arn
+share/gromacs/top/amber96.ff/aminoacids.c.tdb
+share/gromacs/top/amber96.ff/aminoacids.hdb
+share/gromacs/top/amber96.ff/aminoacids.n.tdb
+share/gromacs/top/amber96.ff/aminoacids.r2b
+share/gromacs/top/amber96.ff/aminoacids.rtp
+share/gromacs/top/amber96.ff/aminoacids.vsd
+share/gromacs/top/amber96.ff/atomtypes.atp
+share/gromacs/top/amber96.ff/dna.arn
+share/gromacs/top/amber96.ff/dna.hdb
+share/gromacs/top/amber96.ff/dna.r2b
+share/gromacs/top/amber96.ff/dna.rtp
+share/gromacs/top/amber96.ff/ffbonded.itp
+share/gromacs/top/amber96.ff/ffnonbonded.itp
+share/gromacs/top/amber96.ff/forcefield.doc
+share/gromacs/top/amber96.ff/forcefield.itp
+share/gromacs/top/amber96.ff/gbsa.itp
+share/gromacs/top/amber96.ff/ions.itp
+share/gromacs/top/amber96.ff/rna.arn
+share/gromacs/top/amber96.ff/rna.hdb
+share/gromacs/top/amber96.ff/rna.r2b
+share/gromacs/top/amber96.ff/rna.rtp
+share/gromacs/top/amber96.ff/spc.itp
+share/gromacs/top/amber96.ff/spce.itp
+share/gromacs/top/amber96.ff/tip3p.itp
+share/gromacs/top/amber96.ff/tip4p.itp
+share/gromacs/top/amber96.ff/tip4pew.itp
+share/gromacs/top/amber96.ff/tip5p.itp
+share/gromacs/top/amber96.ff/urea.itp
+share/gromacs/top/amber96.ff/watermodels.dat
+share/gromacs/top/amber99.ff/aminoacids.arn
+share/gromacs/top/amber99.ff/aminoacids.c.tdb
+share/gromacs/top/amber99.ff/aminoacids.hdb
+share/gromacs/top/amber99.ff/aminoacids.n.tdb
+share/gromacs/top/amber99.ff/aminoacids.r2b
+share/gromacs/top/amber99.ff/aminoacids.rtp
+share/gromacs/top/amber99.ff/aminoacids.vsd
+share/gromacs/top/amber99.ff/atomtypes.atp
+share/gromacs/top/amber99.ff/dna.arn
+share/gromacs/top/amber99.ff/dna.hdb
+share/gromacs/top/amber99.ff/dna.r2b
+share/gromacs/top/amber99.ff/dna.rtp
+share/gromacs/top/amber99.ff/ffbonded.itp
+share/gromacs/top/amber99.ff/ffnonbonded.itp
+share/gromacs/top/amber99.ff/forcefield.doc
+share/gromacs/top/amber99.ff/forcefield.itp
+share/gromacs/top/amber99.ff/gbsa.itp
+share/gromacs/top/amber99.ff/ions.itp
+share/gromacs/top/amber99.ff/rna.arn
+share/gromacs/top/amber99.ff/rna.hdb
+share/gromacs/top/amber99.ff/rna.r2b
+share/gromacs/top/amber99.ff/rna.rtp
+share/gromacs/top/amber99.ff/spc.itp
+share/gromacs/top/amber99.ff/spce.itp
+share/gromacs/top/amber99.ff/tip3p.itp
+share/gromacs/top/amber99.ff/tip4p.itp
+share/gromacs/top/amber99.ff/tip4pew.itp
+share/gromacs/top/amber99.ff/tip5p.itp
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+share/gromacs/top/gromos53a5.ff/forcefield.itp
+share/gromacs/top/gromos53a5.ff/ions.itp
+share/gromacs/top/gromos53a5.ff/spc.itp
+share/gromacs/top/gromos53a5.ff/spce.itp
+share/gromacs/top/gromos53a5.ff/tip3p.itp
+share/gromacs/top/gromos53a5.ff/tip4p.itp
+share/gromacs/top/gromos53a5.ff/watermodels.dat
+share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb
+share/gromacs/top/gromos53a6.ff/aminoacids.hdb
+share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb
+share/gromacs/top/gromos53a6.ff/aminoacids.r2b
+share/gromacs/top/gromos53a6.ff/aminoacids.rtp
+share/gromacs/top/gromos53a6.ff/aminoacids.vsd
+share/gromacs/top/gromos53a6.ff/atomtypes.atp
+share/gromacs/top/gromos53a6.ff/ff_dum.itp
+share/gromacs/top/gromos53a6.ff/ffbonded.itp
+share/gromacs/top/gromos53a6.ff/ffnonbonded.itp
+share/gromacs/top/gromos53a6.ff/forcefield.doc
+share/gromacs/top/gromos53a6.ff/forcefield.itp
+share/gromacs/top/gromos53a6.ff/ions.itp
+share/gromacs/top/gromos53a6.ff/spc.itp
+share/gromacs/top/gromos53a6.ff/spce.itp
+share/gromacs/top/gromos53a6.ff/tip3p.itp
+share/gromacs/top/gromos53a6.ff/tip4p.itp
+share/gromacs/top/gromos53a6.ff/watermodels.dat
 share/gromacs/top/gurgle.dat
-share/gromacs/top/h2p4o13.itp
-share/gromacs/top/h2p8o25.itp
-share/gromacs/top/h2po4.itp
 share/gromacs/top/ha-shift.dat
 share/gromacs/top/highway.dat
 share/gromacs/top/ions.itp
 share/gromacs/top/links.dat
-share/gromacs/top/methanol.itp
+share/gromacs/top/oplsaa.ff/1propanol.itp
+share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
+share/gromacs/top/oplsaa.ff/aminoacids.hdb
+share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
+share/gromacs/top/oplsaa.ff/aminoacids.r2b
+share/gromacs/top/oplsaa.ff/aminoacids.rtp
+share/gromacs/top/oplsaa.ff/aminoacids.vsd
+share/gromacs/top/oplsaa.ff/atomname2type.n2t
+share/gromacs/top/oplsaa.ff/atomtypes.atp
+share/gromacs/top/oplsaa.ff/ethanol.itp
+share/gromacs/top/oplsaa.ff/ffbonded.itp
+share/gromacs/top/oplsaa.ff/ffnonbonded.itp
+share/gromacs/top/oplsaa.ff/forcefield.doc
+share/gromacs/top/oplsaa.ff/forcefield.itp
+share/gromacs/top/oplsaa.ff/gbsa.itp
+share/gromacs/top/oplsaa.ff/ions.itp
+share/gromacs/top/oplsaa.ff/methanol.itp
+share/gromacs/top/oplsaa.ff/spc.itp
+share/gromacs/top/oplsaa.ff/spce.itp
+share/gromacs/top/oplsaa.ff/tip3p.itp
+share/gromacs/top/oplsaa.ff/tip4p.itp
+share/gromacs/top/oplsaa.ff/tip5p.itp
+share/gromacs/top/oplsaa.ff/watermodels.dat
 share/gromacs/top/phbres.dat
 share/gromacs/top/ps.m2p
 share/gromacs/top/random.dat
 share/gromacs/top/refi_aa.dat
+share/gromacs/top/residuetypes.dat
+share/gromacs/top/sfactor.dat
 share/gromacs/top/spc.itp
 share/gromacs/top/spc216.gro
 share/gromacs/top/spce.itp
@@ -641,14 +1026,10 @@ share/gromacs/top/table6-11.xvg
 share/gromacs/top/table6-12.xvg
 share/gromacs/top/table6-8.xvg
 share/gromacs/top/table6-9.xvg
-share/gromacs/top/tfe.itp
 share/gromacs/top/tip3p.itp
 share/gromacs/top/tip4p.gro
 share/gromacs/top/tip4p.itp
 share/gromacs/top/tip5p.gro
-share/gromacs/top/tip5p.itp
-share/gromacs/top/urea+h2o.gro
-share/gromacs/top/urea.itp
 share/gromacs/top/vdwradii.dat
 share/gromacs/top/xlateat.dat
 share/gromacs/tutor/gmxdemo/cpeptide.pdb
diff --git a/biology/gromacs/distinfo b/biology/gromacs/distinfo
index 922dd4baa8a..4c16f573f8b 100644
--- a/biology/gromacs/distinfo
+++ b/biology/gromacs/distinfo
@@ -1,16 +1,12 @@
-$NetBSD: distinfo,v 1.4 2010/07/31 19:14:08 dholland Exp $
+$NetBSD: distinfo,v 1.5 2010/09/03 20:52:39 asau Exp $
 
-SHA1 (gromacs-4.0.7.tar.gz) = 8519bef2fa989fb487d54612b0a2d0228f228b30
-RMD160 (gromacs-4.0.7.tar.gz) = 4fa8e5c90f549ef627a98a907a166676692a4c4b
-Size (gromacs-4.0.7.tar.gz) = 8404518 bytes
-SHA1 (patch-aa) = dcf39e862c2087bca0cd4e577438633bf70fe57f
-SHA1 (patch-ab) = 333fea1f0844f8628795f593de16c941744b11d2
-SHA1 (patch-ac) = 164a7b3e06ab4f4cc1142615c1281eec82adee9b
+SHA1 (gromacs-4.5.1.tar.gz) = 4352565278e39fb619208950780d8cb0b470a200
+RMD160 (gromacs-4.5.1.tar.gz) = b28973526859359c84ba5d4fe2a5018b158f932b
+Size (gromacs-4.5.1.tar.gz) = 10300446 bytes
+SHA1 (patch-aa) = 29c6683c71989621f0f41682b1c225f524a2d84f
 SHA1 (patch-ad) = 68b37154ba466e28cad0e539e25253c901421aaa
 SHA1 (patch-ae) = 59a5e88abeee883483b557cab1681c9a9098870f
-SHA1 (patch-af) = 58e97df84e64e071257fd36d09840ef719461ea5
-SHA1 (patch-ag) = 5d46a0dba7db4dbf08ea83d448a6e5201871d217
-SHA1 (patch-ah) = ad930cbb9f448780ca8745b899fe54c5470fff3b
+SHA1 (patch-ag) = 810d58d3ad787c9508f775674541775245402596
+SHA1 (patch-ah) = 36ceeb409e59d8d3f0abe3bfa3ea3108f61f7a8e
 SHA1 (patch-ai) = ed4aa71eb56d1300c67cd17057f72ea452739f3d
 SHA1 (patch-aj) = 080d2923d729ff00de0f2cae75a82ec6c3769d6c
-SHA1 (patch-ak) = bdfebf85422a6a9025d1f2c71921c4cc1c3069c4
diff --git a/biology/gromacs/patches/patch-aa b/biology/gromacs/patches/patch-aa
index 13d6487d231..37e72b12be1 100644
--- a/biology/gromacs/patches/patch-aa
+++ b/biology/gromacs/patches/patch-aa
@@ -1,19 +1,19 @@
-$NetBSD: patch-aa,v 1.1.1.1 2010/03/15 14:08:49 asau Exp $
+$NetBSD: patch-aa,v 1.2 2010/09/03 20:52:39 asau Exp $
 
 Allow flags to contain commas.
 
---- share/template/Makefile.in.orig	2010-01-12 15:44:18.000000000 +0300
-+++ share/template/Makefile.in	2010-01-12 15:58:57.000000000 +0300
-@@ -389,9 +389,9 @@
+--- share/template/Makefile.in.orig	2010-08-10 22:56:17.000000000 +0400
++++ share/template/Makefile.in	2010-08-11 00:14:07.000000000 +0400
+@@ -569,9 +569,9 @@
  
  Makefile.@host@ Makefile.@host@_double: Template.mak Makefile 
  	cat $(srcdir)/Template.mak | \
--	sed 's,@LDFLAGS\@,$(LDFLAGS),' | \
--	sed 's,@LIBS\@,$(LIBS),' | \
+-	sed 's,@LDFLAGS\@,$(XLDFLAGS),' | \
+-	sed 's,@LIBS\@,$(XLIBS),' | \
 -	sed 's,@CFLAGS\@,$(MYCFLAGS),' | \
-+	sed 's|@LDFLAGS\@|$(LDFLAGS)|' | \
-+	sed 's|@LIBS\@|$(LIBS)|' | \
++	sed 's|@LDFLAGS\@|$(XLDFLAGS)|' | \
++	sed 's|@LIBS\@|$(XLIBS)|' | \
 +	sed 's|@CFLAGS\@|$(MYCFLAGS)|' | \
- 	sed 's,@CC\@,$(CC),' | \
+ 	sed 's,@CC\@,$(XCC),' | \
  	sed 's,@host\@,@host@,' >$@
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
+ #template.$(OBJEXT): gromacs
diff --git a/biology/gromacs/patches/patch-ab b/biology/gromacs/patches/patch-ab
deleted file mode 100644
index a25ab310a3c..00000000000
--- a/biology/gromacs/patches/patch-ab
+++ /dev/null
@@ -1,24 +0,0 @@
-$NetBSD: patch-ab,v 1.1.1.1 2010/03/15 14:08:49 asau Exp $
-
-Avoid non-standard "==" in test.
-
---- configure.ac.orig	2009-12-07 00:18:27.000000000 +0300
-+++ configure.ac	2010-03-15 16:02:27.000000000 +0300
-@@ -183,7 +183,7 @@
- 			     [set --enable-ppc-sqrt=1 for better speed.])],,
- 			     enable_ppc_sqrt=no)
- if test "$enable_ppc_sqrt" != "no"; then
--   if test "$enable_ppc_sqrt" == "1"; then
-+   if test "$enable_ppc_sqrt" = "1"; then
-      ppc_sqrt_niter=1;
-    else 
-      ppc_sqrt_niter=2;
-@@ -193,7 +193,7 @@
-    enable_software_sqrt="no";
- fi
- AM_CONDITIONAL([GMX_POWERPC_SQRT],[test "$enable_ppc_sqrt" != "no"])
--AM_CONDITIONAL([GMX_POWERPC_SQRT_SINGLE_ITERATION],[test "$ppc_sqrt_niter" == "1"])
-+AM_CONDITIONAL([GMX_POWERPC_SQRT_SINGLE_ITERATION],[test "$ppc_sqrt_niter" = "1"])
- 
- 
- if test "$enable_software_sqrt" = "yes"; then
diff --git a/biology/gromacs/patches/patch-ac b/biology/gromacs/patches/patch-ac
deleted file mode 100644
index 534f950d288..00000000000
--- a/biology/gromacs/patches/patch-ac
+++ /dev/null
@@ -1,24 +0,0 @@
-$NetBSD: patch-ac,v 1.1.1.1 2010/03/15 14:08:49 asau Exp $
-
-Avoid non-standard "==" in test.
-
---- configure.orig	2010-03-15 15:59:18.000000000 +0300
-+++ configure	2010-03-15 16:00:44.000000000 +0300
-@@ -2994,7 +2994,7 @@
- fi
- 
- if test "$enable_ppc_sqrt" != "no"; then
--   if test "$enable_ppc_sqrt" == "1"; then
-+   if test "$enable_ppc_sqrt" = "1"; then
-      ppc_sqrt_niter=1;
-    else
-      ppc_sqrt_niter=2;
-@@ -3015,7 +3015,7 @@
-   GMX_POWERPC_SQRT_FALSE=
- fi
- 
-- if test "$ppc_sqrt_niter" == "1"; then
-+ if test "$ppc_sqrt_niter" = "1"; then
-   GMX_POWERPC_SQRT_SINGLE_ITERATION_TRUE=
-   GMX_POWERPC_SQRT_SINGLE_ITERATION_FALSE='#'
- else
diff --git a/biology/gromacs/patches/patch-af b/biology/gromacs/patches/patch-af
deleted file mode 100644
index 502ad7e45b8..00000000000
--- a/biology/gromacs/patches/patch-af
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD: patch-af,v 1.1 2010/06/17 09:26:16 asau Exp $
-
-Modern libtool requires tag.
-
---- src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile.in.orig	2009-12-06 21:18:53.000000000 +0000
-+++ src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile.in	2010-06-17 07:53:47.000000000 +0000
-@@ -69,7 +69,7 @@
- 	--mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) \
- 	$(LDFLAGS) -o $@
- CCASCOMPILE = $(CCAS) $(AM_CCASFLAGS) $(CCASFLAGS)
--LTCCASCOMPILE = $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
-+LTCCASCOMPILE = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
- 	--mode=compile $(CCAS) $(AM_CCASFLAGS) $(CCASFLAGS)
- SOURCES = $(libnb_kernel_ia32_3dnow_la_SOURCES)
- DIST_SOURCES = $(libnb_kernel_ia32_3dnow_la_SOURCES)
diff --git a/biology/gromacs/patches/patch-ag b/biology/gromacs/patches/patch-ag
index 18d8bccb310..6c95daf96f7 100644
--- a/biology/gromacs/patches/patch-ag
+++ b/biology/gromacs/patches/patch-ag
@@ -1,11 +1,11 @@
-$NetBSD: patch-ag,v 1.1 2010/06/17 09:26:16 asau Exp $
+$NetBSD: patch-ag,v 1.2 2010/09/03 20:52:39 asau Exp $
 
 Modern libtool requires tag.
 
---- src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile.in.orig	2009-12-06 21:18:53.000000000 +0000
-+++ src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile.in	2010-06-17 07:56:36.000000000 +0000
-@@ -67,7 +67,7 @@
- am__depfiles_maybe = depfiles
+--- src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile.in.orig	2010-07-30 22:55:04.000000000 +0400
++++ src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile.in	2010-07-31 11:57:35.000000000 +0400
+@@ -71,7 +71,7 @@
+ am__mv = mv -f
  CPPASCOMPILE = $(CCAS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
  	$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CCASFLAGS) $(CCASFLAGS)
 -LTCPPASCOMPILE = $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
diff --git a/biology/gromacs/patches/patch-ah b/biology/gromacs/patches/patch-ah
index a123b39e06d..7584cd3acb7 100644
--- a/biology/gromacs/patches/patch-ah
+++ b/biology/gromacs/patches/patch-ah
@@ -1,11 +1,11 @@
-$NetBSD: patch-ah,v 1.1 2010/06/17 09:26:16 asau Exp $
+$NetBSD: patch-ah,v 1.2 2010/09/03 20:52:39 asau Exp $
 
 Modern libtool requires tag.
 
---- src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile.in.orig	2009-12-06 21:18:54.000000000 +0000
-+++ src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile.in	2010-06-17 07:57:43.000000000 +0000
-@@ -67,7 +67,7 @@
- am__depfiles_maybe = depfiles
+--- src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile.in.orig	2010-07-30 22:55:04.000000000 +0400
++++ src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile.in	2010-07-31 11:58:30.000000000 +0400
+@@ -71,7 +71,7 @@
+ am__mv = mv -f
  CPPASCOMPILE = $(CCAS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
  	$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CCASFLAGS) $(CCASFLAGS)
 -LTCPPASCOMPILE = $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
diff --git a/biology/gromacs/patches/patch-ak b/biology/gromacs/patches/patch-ak
deleted file mode 100644
index 3e98cf730fc..00000000000
--- a/biology/gromacs/patches/patch-ak
+++ /dev/null
@@ -1,34 +0,0 @@
-$NetBSD: patch-ak,v 1.1 2010/07/31 19:14:08 dholland Exp $
-
-Disable the extra symlinks like in src/gmxlib/Makefile.in; this makes
-the install behavior uniform for all the libraries.
-
-Note that if re-enabled the references to "libdir" below need DESTDIR
-affixed, or it'll blow up if USE_DESTDIR is set.
-
-
---- src/tools/Makefile.in.orig	2009-12-06 21:18:54.000000000 +0000
-+++ src/tools/Makefile.in
-@@ -1407,14 +1407,14 @@ uninstall-am: uninstall-binPROGRAMS unin
- 
- 
- # link the mpi library to non-mpi names if the latter are not present
--install-exec-hook:
--	libname="libgmxana@LIBSUFFIX@"; \
--	nompi="`echo $$libname | sed -e 's,_mpi,,'`"; \
--	libdir="$(libdir)"; \
--	if echo $$libname | grep mpi >/dev/null ; then \
--	  (cd $$libdir && test -e $$libname.a -a ! -e $$nompi.a && $(LN_S) $$libname.a $$nompi.a ; exit 0); \
--	  (cd $$libdir && test -e $$libname.so -a ! -e $$nompi.so && $(LN_S) $$libname.so $$nompi.so ; exit 0); \
--	fi; 
-+install-exec-hook: ;
-+#	libname="libgmxana@LIBSUFFIX@"; \
-+#	nompi="`echo $$libname | sed -e 's,_mpi,,'`"; \
-+#	libdir="$(libdir)"; \
-+#	if echo $$libname | grep mpi >/dev/null ; then \
-+#	  (cd $$libdir && test -e $$libname.a -a ! -e $$nompi.a && $(LN_S) $$libname.a $$nompi.a ; exit 0); \
-+#	  (cd $$libdir && test -e $$libname.so -a ! -e $$nompi.so && $(LN_S) $$libname.so $$nompi.so ; exit 0); \
-+#	fi; 
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
- # Otherwise a system limit (for SysV at least) may be exceeded.
- .NOEXPORT: