ports/150278: [MAINTAINER] science/gromacs: update to 4.5.1

Florian Smeets flo at kasimir.com
Sat Sep 4 14:10:06 UTC 2010 

>Number:         150278
>Category:       ports
>Synopsis:       [MAINTAINER] science/gromacs: update to 4.5.1
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          maintainer-update
>Submitter-Id:   current-users
>Arrival-Date:   Sat Sep 04 14:10:06 UTC 2010
>Closed-Date:
>Last-Modified:
>Originator:     Florian Smeets
>Release:        FreeBSD 8.1-PRERELEASE amd64
>Organization:
>Environment:
System: FreeBSD mail.solomo.de 8.1-PRERELEASE FreeBSD 8.1-PRERELEASE #1: Fri Jul 23 15:47:09 UTC 2010
>Description:
- Update to 4.5.1

Added file(s):
- files/patch-src__gmxlib__Makefile.in
- files/patch-src__kernel__Makefile.in
- files/patch-src__mdlib__Makefile.in
- files/patch-src__tools__Makefile.in

Generated with FreeBSD Port Tools 0.99
>How-To-Repeat:
>Fix:

--- gromacs-4.5.1.patch begins here ---
diff -ruN --exclude=CVS /usr/ports/science/gromacs.orig/Makefile /usr/ports/science/gromacs/Makefile
--- /usr/ports/science/gromacs.orig/Makefile	2010-09-02 22:19:44.000000000 +0200
+++ /usr/ports/science/gromacs/Makefile	2010-09-04 16:06:46.000000000 +0200
@@ -6,8 +6,7 @@
 #
 
 PORTNAME=	gromacs
-PORTVERSION=	4.0.7
-PORTREVISION=	1
+PORTVERSION=	4.5.1
 CATEGORIES=	science
 MASTER_SITES=	ftp://ftp.gromacs.org/pub/gromacs/
 
@@ -100,13 +99,14 @@
 PLIST_SUB+=	SUFFIX_MPI="" MPI="@comment "
 .endif
 
-MAN1=	anadock.1 \
-	do_dssp.1 \
+MAN1=	do_dssp.1 \
 	editconf.1 \
 	eneconv.1 \
+	g_anadock.1 \
 	g_anaeig.1 \
 	g_analyze.1 \
 	g_angle.1 \
+	g_bar.1 \
 	g_bond.1 \
 	g_bundle.1 \
 	g_chi.1 \
@@ -131,9 +131,9 @@
 	g_hbond.1 \
 	g_helix.1 \
 	g_helixorient.1 \
-	g_kinetics.1 \
 	g_lie.1 \
 	g_mdmat.1 \
+	g_membed.1 \
 	g_mindist.1 \
 	g_morph.1 \
 	g_msd.1 \
@@ -144,26 +144,32 @@
 	g_polystat.1 \
 	g_potential.1 \
 	g_principal.1 \
+	g_protonate.1 \
 	g_rama.1 \
 	g_rdf.1 \
 	g_rms.1 \
 	g_rmsdist.1 \
 	g_rmsf.1 \
 	g_rotacf.1 \
+	g_rotmat.1 \
 	g_saltbr.1 \
 	g_sas.1 \
-	g_sdf.1 \
+	g_select.1 \
 	g_sgangle.1 \
 	g_sham.1 \
+	g_sigeps.1 \
 	g_sorient.1 \
 	g_spatial.1 \
 	g_spol.1 \
 	g_tcaf.1 \
 	g_traj.1 \
+	g_tune_pme.1 \
 	g_vanhove.1 \
 	g_velacc.1 \
 	g_wham.1 \
-	gen_table.1 \
+	g_wheel.1 \
+	g_x2top.1 \
+	g_xrama.1 \
 	genbox.1 \
 	genconf.1 \
 	genion.1 \
@@ -171,22 +177,18 @@
 	gmxcheck.1 \
 	gmxdump.1 \
 	grompp.1 \
-	highway.1 \
 	make_edi.1 \
 	make_ndx.1 \
 	mdrun.1 \
 	mk_angndx.1 \
 	ngmx.1 \
 	pdb2gmx.1 \
-	protonate.1 \
-	sigeps.1 \
 	tpbconv.1 \
 	trjcat.1 \
 	trjconv.1 \
 	trjorder.1 \
-	wheel.1 \
-	x2top.1 \
-	xpm2ps.1 \
-	xrama.1
+	xpm2ps.1
+
+MAN7=	gromacs.7
 
 .include <bsd.port.post.mk>
diff -ruN --exclude=CVS /usr/ports/science/gromacs.orig/distinfo /usr/ports/science/gromacs/distinfo
--- /usr/ports/science/gromacs.orig/distinfo	2010-09-02 22:19:44.000000000 +0200
+++ /usr/ports/science/gromacs/distinfo	2010-09-04 16:06:46.000000000 +0200
@@ -1,3 +1,3 @@
-MD5 (gromacs-4.0.7.tar.gz) = 51369bd553e6bba4085a58bcf23d337d
-SHA256 (gromacs-4.0.7.tar.gz) = 048f8ece2829f01d99f7e04e1d6e8f88d3a32273192274f2e9fcf71f41f212c1
-SIZE (gromacs-4.0.7.tar.gz) = 8404518
+MD5 (gromacs-4.5.1.tar.gz) = d4b737b0bea8a9390d2c3ad9b159914d
+SHA256 (gromacs-4.5.1.tar.gz) = 768a02ee995f950b442dc131c25c1b946f1907d2286fd3fa3eb7fa967ed8efb0
+SIZE (gromacs-4.5.1.tar.gz) = 10304547
diff -ruN --exclude=CVS /usr/ports/science/gromacs.orig/files/patch-src__gmxlib__Makefile.in /usr/ports/science/gromacs/files/patch-src__gmxlib__Makefile.in
--- /usr/ports/science/gromacs.orig/files/patch-src__gmxlib__Makefile.in	1970-01-01 01:00:00.000000000 +0100
+++ /usr/ports/science/gromacs/files/patch-src__gmxlib__Makefile.in	2010-09-04 16:06:44.000000000 +0200
@@ -0,0 +1,11 @@
+--- ./src/gmxlib/Makefile.in.orig	2010-08-23 15:53:16.000000000 +0200
++++ ./src/gmxlib/Makefile.in	2010-08-23 15:53:32.000000000 +0200
+@@ -365,7 +365,7 @@
+ 	gmx_system_xdr.c md5.c vmdio.c vmddlopen.c sighandler.c oenv.c \
+ 	gmxfio_rw.c gmxfio_asc.c gmxfio_bin.c gmxfio_xdr.c \
+ 	$(am__append_1)
+-pkgconfigdir = ${libdir}/pkgconfig
++pkgconfigdir = ${PREFIX}/libdata/pkgconfig
+ pkgconfig_DATA = libgmx at LIBSUFFIX@.pc
+ 
+ # clean all libtool libraries, since the target names might have changed
diff -ruN --exclude=CVS /usr/ports/science/gromacs.orig/files/patch-src__kernel__Makefile.in /usr/ports/science/gromacs/files/patch-src__kernel__Makefile.in
--- /usr/ports/science/gromacs.orig/files/patch-src__kernel__Makefile.in	1970-01-01 01:00:00.000000000 +0100
+++ /usr/ports/science/gromacs/files/patch-src__kernel__Makefile.in	2010-09-04 16:06:45.000000000 +0200
@@ -0,0 +1,11 @@
+--- ./src/kernel/Makefile.in.orig	2010-08-23 15:52:04.000000000 +0200
++++ ./src/kernel/Makefile.in	2010-08-23 15:53:01.000000000 +0200
+@@ -322,7 +322,7 @@
+ top_srcdir = @top_srcdir@
+ AM_CPPFLAGS = -I$(top_srcdir)/include -DGMXLIBDIR=\"$(datadir)/top\"
+ lib_LTLIBRARIES = libgmxpreprocess at LIBSUFFIX@.la 
+-pkgconfigdir = ${libdir}/pkgconfig
++pkgconfigdir = ${PREFIX}/libdata/pkgconfig
+ pkgconfig_DATA = libgmxpreprocess at LIBSUFFIX@.pc
+ EXTRA_DIST = libgmxpreprocess.pc.cmakein
+ LDADD = $(lib_LTLIBRARIES) ../mdlib/libmd at LIBSUFFIX@.la ../gmxlib/libgmx at LIBSUFFIX@.la 
diff -ruN --exclude=CVS /usr/ports/science/gromacs.orig/files/patch-src__mdlib__Makefile.in /usr/ports/science/gromacs/files/patch-src__mdlib__Makefile.in
--- /usr/ports/science/gromacs.orig/files/patch-src__mdlib__Makefile.in	1970-01-01 01:00:00.000000000 +0100
+++ /usr/ports/science/gromacs/files/patch-src__mdlib__Makefile.in	2010-09-04 16:06:45.000000000 +0200
@@ -0,0 +1,11 @@
+--- ./src/mdlib/Makefile.in.orig	2010-08-23 15:53:46.000000000 +0200
++++ ./src/mdlib/Makefile.in	2010-08-23 15:53:58.000000000 +0200
+@@ -262,7 +262,7 @@
+ libmd at LIBSUFFIX@_la_DEPENDENCIES = ../gmxlib/libgmx at LIBSUFFIX@.la	
+ libmd at LIBSUFFIX@_la_LDFLAGS = -no-undefined -version-info @SHARED_VERSION_INFO@ $(FFT_LIBS) $(XML_LIBS) $(PTHREAD_LIBS)
+ lib_LTLIBRARIES = libmd at LIBSUFFIX@.la
+-pkgconfigdir = ${libdir}/pkgconfig
++pkgconfigdir = ${PREFIX}/libdata/pkgconfig
+ pkgconfig_DATA = libmd at LIBSUFFIX@.pc
+ EXTRA_DIST = libmd.pc.cmakein
+ libmd at LIBSUFFIX@_la_SOURCES = \
diff -ruN --exclude=CVS /usr/ports/science/gromacs.orig/files/patch-src__tools__Makefile.in /usr/ports/science/gromacs/files/patch-src__tools__Makefile.in
--- /usr/ports/science/gromacs.orig/files/patch-src__tools__Makefile.in	1970-01-01 01:00:00.000000000 +0100
+++ /usr/ports/science/gromacs/files/patch-src__tools__Makefile.in	2010-09-04 16:06:44.000000000 +0200
@@ -0,0 +1,11 @@
+--- ./src/tools/Makefile.in.orig	2010-08-23 15:51:50.000000000 +0200
++++ ./src/tools/Makefile.in	2010-08-23 15:51:16.000000000 +0200
+@@ -726,7 +726,7 @@
+ top_srcdir = @top_srcdir@
+ AM_CPPFLAGS = -I$(top_srcdir)/include -DGMXLIBDIR=\"$(datadir)/top\"
+ lib_LTLIBRARIES = libgmxana at LIBSUFFIX@.la
+-pkgconfigdir = ${libdir}/pkgconfig
++pkgconfigdir = ${PREFIX}/libdata/pkgconfig
+ pkgconfig_DATA = libgmxana at LIBSUFFIX@.pc
+ EXTRA_DIST = libgmxana.pc.cmakein
+ libgmxana at LIBSUFFIX@_la_LIBADD = ../gmxlib/libgmx at LIBSUFFIX@.la	../mdlib/libmd at LIBSUFFIX@.la	
diff -ruN --exclude=CVS /usr/ports/science/gromacs.orig/pkg-plist /usr/ports/science/gromacs/pkg-plist
--- /usr/ports/science/gromacs.orig/pkg-plist	2010-09-03 14:44:23.000000000 +0200
+++ /usr/ports/science/gromacs/pkg-plist	2010-09-04 16:06:47.000000000 +0200
@@ -2,7 +2,6 @@
 bin/GMXRC.bash
 bin/GMXRC.csh
 bin/GMXRC.zsh
-bin/anadock
 bin/completion.bash
 bin/completion.csh
 bin/completion.zsh
@@ -10,9 +9,11 @@
 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
@@ -37,9 +38,10 @@
 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
@@ -47,28 +49,36 @@
 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
+%%X11%%bin/g_xrama
 bin/genbox
 bin/genconf
 bin/genion
@@ -76,25 +86,18 @@
 bin/gmxcheck
 bin/gmxdump
 bin/grompp
-%%X11%%bin/highway
-bin/luck
 bin/make_edi
 bin/make_ndx
 bin/mdrun
 bin/mk_angndx
 %%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
-%%X11%%bin/xrama
 include/gromacs/3dview.h
 include/gromacs/assert.h
 include/gromacs/atomprop.h
@@ -102,12 +105,15 @@
 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
@@ -116,45 +122,60 @@
 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
@@ -162,14 +183,17 @@
 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
@@ -177,29 +201,54 @@
 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/cycles.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/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
@@ -212,6 +261,7 @@
 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
@@ -221,10 +271,10 @@
 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
@@ -234,11 +284,14 @@
 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
@@ -248,17 +301,23 @@
 lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.a
 lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.la
 lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.so
-lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.so.5
-%%MPI%%lib/libgmxana%%SUFFIX_D%%.a
-%%MPI%%lib/libgmxana%%SUFFIX_D%%.so
+lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6
 lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.a
 lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.la
 lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.so
-lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.so.5
+lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6
+lib/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.a
+lib/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.la
+lib/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.so
+lib/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6
 lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.a
 lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.la
 lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.so
-lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.so.5
+lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6
+libdata/pkgconfig/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
+libdata/pkgconfig/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
+libdata/pkgconfig/libgmxpreprocess%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
+libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 %%DATADIR%%/html/gmxfaq.html
 %%DATADIR%%/html/images/1ctf-0.2.jpg
 %%DATADIR%%/html/images/1ctf-0.5.jpg
@@ -415,142 +474,467 @@
 %%DATADIR%%/html/online/xvg.html
 %%DATADIR%%/html/online/yourown.html
 %%DATADIR%%/template/Makefile.%%BUILD%%%%SUFFIX_DOUBLE%%
+%%DATADIR%%/template/Makefile.pkg
 %%DATADIR%%/template/README
 %%DATADIR%%/template/template.c
-%%DATADIR%%/top/1mlg.itp
-%%DATADIR%%/top/2mlg.itp
-%%DATADIR%%/top/FF.dat
-%%DATADIR%%/top/aminoacids.dat
+%%DATADIR%%/top/amber03.ff/aminoacids.arn
+%%DATADIR%%/top/amber03.ff/aminoacids.c.tdb
+%%DATADIR%%/top/amber03.ff/aminoacids.hdb
+%%DATADIR%%/top/amber03.ff/aminoacids.n.tdb
+%%DATADIR%%/top/amber03.ff/aminoacids.r2b
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+%%DATADIR%%/top/gmx.ff/ff_dum.itp
+%%DATADIR%%/top/gmx.ff/ffbonded.itp
+%%DATADIR%%/top/gmx.ff/ffnonbonded.itp
+%%DATADIR%%/top/gmx.ff/forcefield.doc
+%%DATADIR%%/top/gmx.ff/forcefield.itp
+%%DATADIR%%/top/gmx.ff/h2p4o13.itp
+%%DATADIR%%/top/gmx.ff/h2p8o25.itp
+%%DATADIR%%/top/gmx.ff/h2po4.itp
+%%DATADIR%%/top/gmx.ff/ions.itp
+%%DATADIR%%/top/gmx.ff/spc.itp
+%%DATADIR%%/top/gmx.ff/spce.itp
+%%DATADIR%%/top/gmx.ff/tfe.itp
+%%DATADIR%%/top/gmx.ff/tip3p.itp
+%%DATADIR%%/top/gmx.ff/tip4p.itp
+%%DATADIR%%/top/gmx.ff/watermodels.dat
+%%DATADIR%%/top/gmx2.ff/aminoacids.c.tdb
+%%DATADIR%%/top/gmx2.ff/aminoacids.hdb
+%%DATADIR%%/top/gmx2.ff/aminoacids.n.tdb
+%%DATADIR%%/top/gmx2.ff/aminoacids.rtp
+%%DATADIR%%/top/gmx2.ff/aminoacids.vsd
+%%DATADIR%%/top/gmx2.ff/atomtypes.atp
+%%DATADIR%%/top/gmx2.ff/ff_dum.itp
+%%DATADIR%%/top/gmx2.ff/ffbonded.itp
+%%DATADIR%%/top/gmx2.ff/ffnonbonded.itp
+%%DATADIR%%/top/gmx2.ff/forcefield.doc
+%%DATADIR%%/top/gmx2.ff/forcefield.itp
+%%DATADIR%%/top/gmx2.ff/ions.itp
+%%DATADIR%%/top/gmx2.ff/spc.itp
+%%DATADIR%%/top/gmx2.ff/spce.itp
+%%DATADIR%%/top/gmx2.ff/tip3p.itp
+%%DATADIR%%/top/gmx2.ff/tip4p.itp
+%%DATADIR%%/top/gmx2.ff/watermodels.dat
+%%DATADIR%%/top/gromos43a1.ff/aminoacids.c.tdb
+%%DATADIR%%/top/gromos43a1.ff/aminoacids.hdb
+%%DATADIR%%/top/gromos43a1.ff/aminoacids.n.tdb
+%%DATADIR%%/top/gromos43a1.ff/aminoacids.r2b
+%%DATADIR%%/top/gromos43a1.ff/aminoacids.rtp
+%%DATADIR%%/top/gromos43a1.ff/aminoacids.vsd
+%%DATADIR%%/top/gromos43a1.ff/atomtypes.atp
+%%DATADIR%%/top/gromos43a1.ff/ff_dum.itp
+%%DATADIR%%/top/gromos43a1.ff/ffbonded.itp
+%%DATADIR%%/top/gromos43a1.ff/ffnonbonded.itp
+%%DATADIR%%/top/gromos43a1.ff/forcefield.doc
+%%DATADIR%%/top/gromos43a1.ff/forcefield.itp
+%%DATADIR%%/top/gromos43a1.ff/ions.itp
+%%DATADIR%%/top/gromos43a1.ff/methanol.itp
+%%DATADIR%%/top/gromos43a1.ff/methanol216.gro
+%%DATADIR%%/top/gromos43a1.ff/spc.itp
+%%DATADIR%%/top/gromos43a1.ff/spce.itp
+%%DATADIR%%/top/gromos43a1.ff/tip3p.itp
+%%DATADIR%%/top/gromos43a1.ff/tip4p.itp
+%%DATADIR%%/top/gromos43a1.ff/watermodels.dat
+%%DATADIR%%/top/gromos43a2.ff/aminoacids.c.tdb
+%%DATADIR%%/top/gromos43a2.ff/aminoacids.hdb
+%%DATADIR%%/top/gromos43a2.ff/aminoacids.n.tdb
+%%DATADIR%%/top/gromos43a2.ff/aminoacids.r2b
+%%DATADIR%%/top/gromos43a2.ff/aminoacids.rtp
+%%DATADIR%%/top/gromos43a2.ff/aminoacids.vsd
+%%DATADIR%%/top/gromos43a2.ff/atomtypes.atp
+%%DATADIR%%/top/gromos43a2.ff/ff_dum.itp
+%%DATADIR%%/top/gromos43a2.ff/ffbonded.itp
+%%DATADIR%%/top/gromos43a2.ff/ffnonbonded.itp
+%%DATADIR%%/top/gromos43a2.ff/forcefield.doc
+%%DATADIR%%/top/gromos43a2.ff/forcefield.itp
+%%DATADIR%%/top/gromos43a2.ff/ions.itp
+%%DATADIR%%/top/gromos43a2.ff/spc.itp
+%%DATADIR%%/top/gromos43a2.ff/spce.itp
+%%DATADIR%%/top/gromos43a2.ff/tip3p.itp
+%%DATADIR%%/top/gromos43a2.ff/tip4p.itp
+%%DATADIR%%/top/gromos43a2.ff/watermodels.dat
+%%DATADIR%%/top/gromos45a3.ff/aminoacids.c.tdb
+%%DATADIR%%/top/gromos45a3.ff/aminoacids.hdb
+%%DATADIR%%/top/gromos45a3.ff/aminoacids.n.tdb
+%%DATADIR%%/top/gromos45a3.ff/aminoacids.r2b
+%%DATADIR%%/top/gromos45a3.ff/aminoacids.rtp
+%%DATADIR%%/top/gromos45a3.ff/aminoacids.vsd
+%%DATADIR%%/top/gromos45a3.ff/atomtypes.atp
+%%DATADIR%%/top/gromos45a3.ff/ff_dum.itp
+%%DATADIR%%/top/gromos45a3.ff/ffbonded.itp
+%%DATADIR%%/top/gromos45a3.ff/ffnonbonded.itp
+%%DATADIR%%/top/gromos45a3.ff/forcefield.doc
+%%DATADIR%%/top/gromos45a3.ff/forcefield.itp
+%%DATADIR%%/top/gromos45a3.ff/ions.itp
+%%DATADIR%%/top/gromos45a3.ff/spc.itp
+%%DATADIR%%/top/gromos45a3.ff/spce.itp
+%%DATADIR%%/top/gromos45a3.ff/tip3p.itp
+%%DATADIR%%/top/gromos45a3.ff/tip4p.itp
+%%DATADIR%%/top/gromos45a3.ff/watermodels.dat
+%%DATADIR%%/top/gromos53a5.ff/aminoacids.c.tdb
+%%DATADIR%%/top/gromos53a5.ff/aminoacids.hdb
+%%DATADIR%%/top/gromos53a5.ff/aminoacids.n.tdb
+%%DATADIR%%/top/gromos53a5.ff/aminoacids.r2b
+%%DATADIR%%/top/gromos53a5.ff/aminoacids.rtp
+%%DATADIR%%/top/gromos53a5.ff/aminoacids.vsd
+%%DATADIR%%/top/gromos53a5.ff/atomname2type.n2t
+%%DATADIR%%/top/gromos53a5.ff/atomtypes.atp
+%%DATADIR%%/top/gromos53a5.ff/ff_dum.itp
+%%DATADIR%%/top/gromos53a5.ff/ffbonded.itp
+%%DATADIR%%/top/gromos53a5.ff/ffnonbonded.itp
+%%DATADIR%%/top/gromos53a5.ff/forcefield.doc
+%%DATADIR%%/top/gromos53a5.ff/forcefield.itp
+%%DATADIR%%/top/gromos53a5.ff/ions.itp
+%%DATADIR%%/top/gromos53a5.ff/spc.itp
+%%DATADIR%%/top/gromos53a5.ff/spce.itp
+%%DATADIR%%/top/gromos53a5.ff/tip3p.itp
+%%DATADIR%%/top/gromos53a5.ff/tip4p.itp
+%%DATADIR%%/top/gromos53a5.ff/watermodels.dat
+%%DATADIR%%/top/gromos53a6.ff/aminoacids.c.tdb
+%%DATADIR%%/top/gromos53a6.ff/aminoacids.hdb
+%%DATADIR%%/top/gromos53a6.ff/aminoacids.n.tdb
+%%DATADIR%%/top/gromos53a6.ff/aminoacids.r2b
+%%DATADIR%%/top/gromos53a6.ff/aminoacids.rtp
+%%DATADIR%%/top/gromos53a6.ff/aminoacids.vsd
+%%DATADIR%%/top/gromos53a6.ff/atomtypes.atp
+%%DATADIR%%/top/gromos53a6.ff/ff_dum.itp
+%%DATADIR%%/top/gromos53a6.ff/ffbonded.itp
+%%DATADIR%%/top/gromos53a6.ff/ffnonbonded.itp
+%%DATADIR%%/top/gromos53a6.ff/forcefield.doc
+%%DATADIR%%/top/gromos53a6.ff/forcefield.itp
+%%DATADIR%%/top/gromos53a6.ff/ions.itp
+%%DATADIR%%/top/gromos53a6.ff/spc.itp
+%%DATADIR%%/top/gromos53a6.ff/spce.itp
+%%DATADIR%%/top/gromos53a6.ff/tip3p.itp
+%%DATADIR%%/top/gromos53a6.ff/tip4p.itp
+%%DATADIR%%/top/gromos53a6.ff/watermodels.dat
 %%DATADIR%%/top/gurgle.dat
-%%DATADIR%%/top/h2p4o13.itp
-%%DATADIR%%/top/h2p8o25.itp
-%%DATADIR%%/top/h2po4.itp
 %%DATADIR%%/top/ha-shift.dat
 %%DATADIR%%/top/highway.dat
 %%DATADIR%%/top/ions.itp
 %%DATADIR%%/top/links.dat
-%%DATADIR%%/top/methanol.itp
+%%DATADIR%%/top/oplsaa.ff/1propanol.itp
+%%DATADIR%%/top/oplsaa.ff/aminoacids.c.tdb
+%%DATADIR%%/top/oplsaa.ff/aminoacids.hdb
+%%DATADIR%%/top/oplsaa.ff/aminoacids.n.tdb
+%%DATADIR%%/top/oplsaa.ff/aminoacids.r2b
+%%DATADIR%%/top/oplsaa.ff/aminoacids.rtp
+%%DATADIR%%/top/oplsaa.ff/aminoacids.vsd
+%%DATADIR%%/top/oplsaa.ff/atomname2type.n2t
+%%DATADIR%%/top/oplsaa.ff/atomtypes.atp
+%%DATADIR%%/top/oplsaa.ff/ethanol.itp
+%%DATADIR%%/top/oplsaa.ff/ffbonded.itp
+%%DATADIR%%/top/oplsaa.ff/ffnonbonded.itp
+%%DATADIR%%/top/oplsaa.ff/forcefield.doc
+%%DATADIR%%/top/oplsaa.ff/forcefield.itp
+%%DATADIR%%/top/oplsaa.ff/gbsa.itp
+%%DATADIR%%/top/oplsaa.ff/ions.itp
+%%DATADIR%%/top/oplsaa.ff/methanol.itp
+%%DATADIR%%/top/oplsaa.ff/spc.itp
+%%DATADIR%%/top/oplsaa.ff/spce.itp
+%%DATADIR%%/top/oplsaa.ff/tip3p.itp
+%%DATADIR%%/top/oplsaa.ff/tip4p.itp
+%%DATADIR%%/top/oplsaa.ff/tip5p.itp
+%%DATADIR%%/top/oplsaa.ff/watermodels.dat
 %%DATADIR%%/top/phbres.dat
 %%DATADIR%%/top/ps.m2p
 %%DATADIR%%/top/random.dat
 %%DATADIR%%/top/refi_aa.dat
+%%DATADIR%%/top/residuetypes.dat
+%%DATADIR%%/top/sfactor.dat
 %%DATADIR%%/top/spc.itp
 %%DATADIR%%/top/spc216.gro
 %%DATADIR%%/top/spce.itp
@@ -563,14 +947,10 @@
 %%DATADIR%%/top/table6-12.xvg
 %%DATADIR%%/top/table6-8.xvg
 %%DATADIR%%/top/table6-9.xvg
-%%DATADIR%%/top/tfe.itp
 %%DATADIR%%/top/tip3p.itp
 %%DATADIR%%/top/tip4p.gro
 %%DATADIR%%/top/tip4p.itp
 %%DATADIR%%/top/tip5p.gro
-%%DATADIR%%/top/tip5p.itp
-%%DATADIR%%/top/urea+h2o.gro
-%%DATADIR%%/top/urea.itp
 %%DATADIR%%/top/vdwradii.dat
 %%DATADIR%%/top/xlateat.dat
 %%DATADIR%%/tutor/gmxdemo/cpeptide.pdb
@@ -612,6 +992,24 @@
 @dirrm %%DATADIR%%/tutor/methanol
 @dirrm %%DATADIR%%/tutor/gmxdemo
 @dirrm %%DATADIR%%/tutor
+ at dirrm %%DATADIR%%/top/oplsaa.ff
+ at dirrm %%DATADIR%%/top/gromos53a6.ff
+ at dirrm %%DATADIR%%/top/gromos53a5.ff
+ at dirrm %%DATADIR%%/top/gromos45a3.ff
+ at dirrm %%DATADIR%%/top/gromos43a2.ff
+ at dirrm %%DATADIR%%/top/gromos43a1.ff
+ at dirrm %%DATADIR%%/top/gmx2.ff
+ at dirrm %%DATADIR%%/top/gmx.ff
+ at dirrm %%DATADIR%%/top/encadv.ff
+ at dirrm %%DATADIR%%/top/encads.ff
+ at dirrm %%DATADIR%%/top/charmm27.ff
+ at dirrm %%DATADIR%%/top/amberGS.ff
+ at dirrm %%DATADIR%%/top/amber99sb.ff
+ at dirrm %%DATADIR%%/top/amber99sb-ildn.ff
+ at dirrm %%DATADIR%%/top/amber99.ff
+ at dirrm %%DATADIR%%/top/amber96.ff
+ at dirrm %%DATADIR%%/top/amber94.ff
+ at dirrm %%DATADIR%%/top/amber03.ff
 @dirrm %%DATADIR%%/top
 @dirrm %%DATADIR%%/template
 @dirrm %%DATADIR%%/html/online
@@ -619,4 +1017,6 @@
 @dirrm %%DATADIR%%/html
 @dirrm %%DATADIR%%
 @dirrm include/gromacs/types
+ at dirrm include/gromacs/thread_mpi/atomic
+ at dirrm include/gromacs/thread_mpi
 @dirrm include/gromacs
--- gromacs-4.5.1.patch ends here ---

>Release-Note:
>Audit-Trail:
>Unformatted:

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