science/vmd: update to 1.9.3

 - update MASTER_SITES to use upstream stride (the old - repackages - sources
   were no longer working).
 - take maintainership: although I don't use the software I am happy to respond
   to PR's and check for updates periodically,
 - add license information for each source:
   - vmd: custom license that requires the user to explicitly download (and
          accept the license before downloading).  Mark the license as
          auto-accept here as the present of the DISTFILE will indicate that
          the license has been accepted
   - tachyon: standard 3-clause BSD license :-)
   - stride: almost BSD license, except only for academic use (i.e.
             non-commersial) and a requirement to report bugs to the author.
             Add a plain text copy of the license file to the port.
   - add missing dependencies: gl, x11
   - fix detection of python.
   - simplify configure patch.
   - update pkg-plist for changes in plugin versions.

5 files changed, 520 insertions, 428 deletions

diff --git a/science/vmd/Makefile b/science/vmd/Makefile
index 2ae9940b7a6e..6e5af3beaf59 100644
--- a/science/vmd/Makefile
+++ b/science/vmd/Makefile
@@ -2,19 +2,22 @@
 # $FreeBSD$
 
 PORTNAME=	vmd
-DISTVERSION=	1.9.1
-PORTREVISION=	5
+DISTVERSION=	1.9.3
 CATEGORIES=	science graphics python tcl tk
-MASTER_SITES=	http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.99b2/:tachyon \
-		http://www.photonlimited.com/~johns/tachyon/files/0.99b2/:tachyon \
-		http://www.ks.uiuc.edu/Research/vmd/extsrcs/:stride
+MASTER_SITES=	http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.99b6/:tachyon \
+		http://www.photonlimited.com/~johns/tachyon/files/0.99b6/:tachyon \
+		http://webclu.bio.wzw.tum.de/stride/:stride \
+		ftp://ftp.ebi.ac.uk/pub/software/unix/stride/src/:stride
 DISTFILES=	${VMD_DIST} \
 		${TACHYON_DIST}:tachyon \
 		${STRIDE_DIST}:stride
 
-MAINTAINER=	ports@FreeBSD.org
+MAINTAINER=	dbn@FreeBSD.org
 COMMENT=	Molecular visualization program
 
+LICENSE=	VMD BSD3CLAUSE STRIDE
+LICENSE_COMB=	multi
+
 BUILD_DEPENDS=	makedepend:devel/makedepend \
 		${PYNUMERIC}
 LIB_DEPENDS=	libtcl85.so:lang/tcl85 \
@@ -23,18 +26,37 @@ LIB_DEPENDS=	libtcl85.so:lang/tcl85 \
 		libnetcdf.so:science/netcdf
 RUN_DEPENDS=	${PYNUMERIC}
 
+LICENSE_FILE_VMD=	${WRKSRC}/LICENSE
+LICENSE_PERMS_VMD=	auto-accept
+LICENSE_NAME_VMD=	Visaul Molecular Dynamics Software License Agreement
+LICENSE_DISTFILES_VMD=	${VMD_DIST}
+
+LICENSE_FILE_BSD3CLAUSE=	${WRKSRC}/lib/tachyon/Copyright
+LICENSE_DISTFILES_BSD3CLAUSE=	${TACHYON_DIST}
+
+LICENSE_TEXT_STRIDE=	${FILESDIR}/stride.txt
+LICENSE_PERMS_STRIDE=	dist-mirror pkg-mirror auto-accept
+LICENSE_NAME_STRIDE=	Stride Copyright Notice
+LICENSE_DISTFILES_STRIDE=${STRIDE_DIST}
+
 USES=		gmake perl5 python
+
 USE_PERL5=	build
-USE_GL=		glu
-USE_GCC=	any
+USE_GL=		gl glu
+USE_XORG=	x11
 
 ONLY_FOR_ARCHS=	i386 amd64
 
-RESTRICTED=	License has restrictions
+CONFIGURE_ENV=	PYTHON_INCLUDE_DIR=${PYTHON_INCLUDEDIR} \
+		PYTHON_LIBRARY_DIR=${PYTHON_LIBDIR} \
+		NUMPY_INCLUDE_DIR=${PYTHON_SITELIBDIR}/numpy/core/include \
+		NUMPY_LIBRARY_DIR=${PYTHON_SITELIBDIR}
+INSTALL_WRKSRC=	${WRKSRC}/src
 
 VMD_DIST=	${PORTNAME}-${DISTVERSION}.src.tar.gz
-TACHYON_DIST=	tachyon-0.99b2.tar.gz
-STRIDE_DIST=	Stride_src.tar.Z
+TACHYON_DIST=	tachyon-0.99b6.tar.gz
+STRIDE_DIST=	stride.tar.gz
+STRIDE_DOC=	stride.doc
 
 .include <bsd.port.pre.mk>
 
@@ -58,7 +80,7 @@ IGNORE=	license restrictions require manual fetching of the distribution\
 .endif
 
 do-extract:
-	${MKDIR} ${WRKDIR}
+	${MKDIR} ${WRKDIR} ${WRKSRC}/lib/stride
 	${TAR} -xzf ${DISTDIR}/${VMD_DIST} -C ${WRKDIR}
 	${TAR} -xzf ${WRKSRC}/lib/surf/surf.tar.Z -C ${WRKSRC}/lib/surf
 	${TAR} -xzf ${DISTDIR}/${TACHYON_DIST} -C ${WRKSRC}/lib
@@ -68,10 +90,10 @@ post-patch:
 	${REINPLACE_CMD} \
 		-e "s|-ltk8.5|-ltk85|" \
 		-e "s|-ltcl8.5|-ltcl85|" \
-		-e "s%\$$python_dir/lib_\$$config_arch%${PREFIX}%" \
-		-e "s|python2.5|${PYTHON_VERSION}|" \
+		-e "s|-lpython2.5|-l${PYTHON_VERSION}${PYTHON_ABIVER}|" \
 		-e "s|%%PREFIX%%|${PREFIX}|g" \
 		-e "s|/usr/local|${LOCALBASE}|g"  \
+		-e "s|-fno-for-scope||g" \
 		${WRKSRC}/configure
 	${REINPLACE_CMD} "s/\"gcc\"/\"${CC}\"/;s/\"g++\"/\"${CXX}\"/" \
 		${WRKSRC}/configure
@@ -85,18 +107,18 @@ post-patch:
 		${WRKSRC}/lib/stride/Makefile \
 		${WRKSRC}/lib/surf/Makefile \
 		${WRKSRC}/lib/tachyon/unix/Make-arch \
-		${WRKDIR}/plugins/cionize/mcudahacks/Makefile.specialbuilds \
 		${WRKDIR}/plugins/cionize/Makefile.specialbuilds \
 		${WRKDIR}/plugins/cionize/Makefile.mine \
 		${WRKDIR}/plugins/cionize/Makefile.testing \
 		${WRKDIR}/plugins/Make-arch \
 		${WRKDIR}/plugins/molfile_plugin/f77/Makefile
 	${REINPLACE_CMD} -E "s/(CXX[[:space:]]*=[[:space:]]*)g\+\+/\1${CXX}/" \
-		${WRKDIR}/plugins/cionize/Makefile.specialbuilds \
 		${WRKDIR}/plugins/fmtool/Makefile.specialbuilds \
 		${WRKDIR}/plugins/hesstrans/src/foo/Makefile \
 		${WRKDIR}/plugins/hesstrans/src/foo/nm_gnu.mak \
 		${WRKDIR}/plugins/Make-arch
+	${REINPLACE_CMD} -e "s/return *;/return 0;/g" \
+		${WRKSRC}/lib/surf/*.c
 
 do-build:
 	${SETENV} ${MAKE_ENV} ${MAKE_CMD} bsd -C ${WRKSRC}/lib/tachyon/unix \
@@ -118,13 +140,12 @@ do-build:
 		&& ${MV} ${WRKSRC}/lib/stride/stride \
 			${WRKSRC}/lib/stride/stride_${VMD_ARCH}
 
-do-install:
-	${SETENV} ${MAKE_ENV} DESTDIR=${STAGEDIR} \
-	    ${MAKE_CMD} -C ${WRKSRC}/src install
+post-install:
+	${REINPLACE_CMD} -i '' -e 's|${STAGEDIR}||g' ${STAGEDIR}${PREFIX}/bin/vmd
 	${STRIP_CMD} ${STAGEDIR}${LOCALBASE}/lib/vmd/*${VMD_ARCH} \
 	    ${STAGEDIR}${LOCALBASE}/lib/vmd/plugins/${VMD_ARCH}/molfile/*.so
-.for f in tcl/autopsf1.3/psfcheck.so tcl/hesstrans1.0/hesstrans.so \
-	  tcl/mutator1.4/libalchemify.so tcl/pmepot1.0/libpmepot.so \
+.for f in tcl/autopsf1.6/psfcheck.so tcl/hesstrans1.0/hesstrans.so \
+	  tcl/mutator1.5/libalchemify.so tcl/pmepot1.0/libpmepot.so \
 	  tcl/psfgen1.6/libpsfgen.so tcl/rnaview1.1/rnaview \
 	  tcl/signalproc1.1/specden.so tcl/signalproc1.1/fftcmds.so \
 	  tcl/signalproc1.1/sgsmooth.so tcl/volutil1.3/volutil \
@@ -133,7 +154,8 @@ do-install:
 	  tcl/libbiokit1.1/structqr tcl/libbiokit1.1/qpair \
 	  tcl/libbiokit1.1/rmsd tcl/libbiokit1.1/percid \
 	  tcl/phylotree1.2/upgmaclu tcl/stamp1.2/stamp \
-	  bin/catdcd4.0/catdcd bin/cionize1.0/cionize
+	  tcl/bossconvert1.0/Topology \
+	  bin/catdcd5.1/catdcd bin/cionize1.0/cionize
 	${STRIP_CMD} ${STAGEDIR}${LOCALBASE}/lib/vmd/plugins/${VMD_ARCH}/${f}
 .endfor
 
diff --git a/science/vmd/distinfo b/science/vmd/distinfo
index d86f624a7010..5d42d032ddd2 100644
--- a/science/vmd/distinfo
+++ b/science/vmd/distinfo
@@ -1,6 +1,7 @@
-SHA256 (vmd-1.9.1.src.tar.gz) = 54aa88e03d86d763383e7b98592a152c9d68e78383e13af0dd2aca09b002491f
-SIZE (vmd-1.9.1.src.tar.gz) = 30748110
-SHA256 (tachyon-0.99b2.tar.gz) = 3bd8dd6ad78c6b2153e985645b385357eb42f3908a2269a7cfe7f9afa35da012
-SIZE (tachyon-0.99b2.tar.gz) = 3352908
-SHA256 (Stride_src.tar.Z) = c40f7de64947ebab7ec49511c0d264b08bc0fcbc703014bdc85d83a7389be230
-SIZE (Stride_src.tar.Z) = 100329
+TIMESTAMP = 1482469862
+SHA256 (vmd-1.9.3.src.tar.gz) = 5bdc314dc836d620fe510ed4b6c3dbe3cf66525b61680ffec4e2563cf495f128
+SIZE (vmd-1.9.3.src.tar.gz) = 43981314
+SHA256 (tachyon-0.99b6.tar.gz) = f4dcaf9c76a4f49310f56254390f9611c22e353947a1745a8c623e8bc8119b97
+SIZE (tachyon-0.99b6.tar.gz) = 2981568
+SHA256 (stride.tar.gz) = 51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a
+SIZE (stride.tar.gz) = 318997
diff --git a/science/vmd/files/patch-configure b/science/vmd/files/patch-configure
index 0ce4ed2e20d9..6db1b98b3627 100644
--- a/science/vmd/files/patch-configure
+++ b/science/vmd/files/patch-configure
@@ -1,19 +1,19 @@
---- configure.orig	2012-02-02 16:53:54.000000000 +0900
-+++ configure	2014-08-28 16:42:38.000000000 +0900
+--- configure.orig	2016-12-01 07:11:33 UTC
++++ configure
 @@ -13,10 +13,10 @@
  $install_name = "vmd";
  
  # Directory where VMD startup script is installed, should be in users' paths.
 -$install_bin_dir="/usr/local/bin";
-+$install_bin_dir="%%PREFIX%%/bin";
++$install_bin_dir="\${DESTDIR}%%PREFIX%%/bin";
  
  # Directory where VMD files and executables are installed
 -$install_library_dir="/usr/local/lib/$install_name";
-+$install_library_dir="%%PREFIX%%/lib/$install_name";
++$install_library_dir="\${DESTDIR}%%PREFIX%%/lib/$install_name";
  
  
  # optionally override hard-coded defaults above with environment variables
-@@ -788,8 +788,8 @@
+@@ -1105,8 +1105,8 @@ if ($config_liboptix) {
  # This may be commented out if not required.
  $libtachyon_defines     = "-DVMDLIBTACHYON";
  $libtachyon_dir         = "$vmd_library_dir/tachyon";
@@ -24,12 +24,12 @@
  $libtachyon_libs        = "-ltachyon";
  @libtachyon_cc          = ();
  @libtachyon_cu          = ();
-@@ -2942,10 +2942,10 @@
+@@ -3187,10 +3187,10 @@ DEFINES     = $DEFINES
  
  # compiler and compiler directives 
  CC          = $arch_cc
 -CFLAGS      = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
-+CFLAGS      += $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
++CFLAGS      = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
  
  CCPP	    = $arch_ccpp
 -CPPFLAGS    = $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
@@ -37,72 +37,3 @@
  
  NVCC        = $arch_nvcc
  NVCCFLAGS   = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
-@@ -2997,38 +2997,38 @@
- 	\$(COMPILERC) \$(RCFLAGS)
- 
- install:
--	if [ ! -d "$install_library_dir" ]; then \\
--		\$(MAKEDIR) "$install_library_dir" ; \\
-+	if [ ! -d "\${DESTDIR}$install_library_dir" ]; then \\
-+		\$(MAKEDIR) "\${DESTDIR}$install_library_dir" ; \\
- 	fi ; \\
--	if [ ! -d "$install_bin_dir" ]; then \\
--		\$(MAKEDIR) "$install_bin_dir" ; \\
-+	if [ ! -d "\${DESTDIR}$install_bin_dir" ]; then \\
-+		\$(MAKEDIR) "\${DESTDIR}$install_bin_dir" ; \\
- 	fi ; \\
--	if [ ! -d "$install_library_dir"/doc ]; then \\
--		\$(MAKEDIR) "$install_library_dir"/doc; \\
-+	if [ ! -d "\${DESTDIR}$install_library_dir"/doc ]; then \\
-+		\$(MAKEDIR) "\${DESTDIR}$install_library_dir"/doc; \\
- 	fi
--	-\$(COPY) ../Announcement  "$install_library_dir"
--	-\$(COPY) ../README        "$install_library_dir"
--	-\$(COPY) ../LICENSE       "$install_library_dir"
--	-\$(COPY) $vmd_doc_dir/ug.pdf        "$install_library_dir"/doc
--	if [ -f $install_library_dir/$config_progname ]; then \\
--           \$(MOVE) "$install_library_dir/$config_progname" "$install_library_dir/OLD_$config_progname" ; \$(DELETE) "$install_library_dir/OLD_$config_progname" ; fi
--	-\$(COPY) ../$config_arch/$config_progname "$install_library_dir"
-+	-\$(COPY) ../Announcement  "\${DESTDIR}$install_library_dir"
-+	-\$(COPY) ../README        "\${DESTDIR}$install_library_dir"
-+	-\$(COPY) ../LICENSE       "\${DESTDIR}$install_library_dir"
-+	-\$(COPY) $vmd_doc_dir/ug.pdf        "\${DESTDIR}$install_library_dir"/doc
-+	if [ -f \${DESTDIR}$install_library_dir/$config_progname ]; then \\
-+           \$(MOVE) "\${DESTDIR}$install_library_dir/$config_progname" "\${DESTDIR}$install_library_dir/OLD_$config_progname" ; \$(DELETE) "\${DESTDIR}$install_library_dir/OLD_$config_progname" ; fi
-+	-\$(COPY) ../$config_arch/$config_progname "\${DESTDIR}$install_library_dir"
- 	if [ -d "../lib/redistrib/lib_$config_arch" ]; then \\
- 		\$(CD) ../lib/redistrib/lib_$config_arch; \$(TAR) -cf - ./* | \\
--		(cd "$install_library_dir" ; \$(TAR) -xf -) \\
-+		(cd "\${DESTDIR}$install_library_dir" ; \$(TAR) -xf -) \\
- 	fi ;
--	-\$(COPY) @vmd_other_exe "$install_library_dir"
-+	-\$(COPY) @vmd_other_exe "\${DESTDIR}$install_library_dir"
- 	-\$(CD) ..; \$(TAR) -cf - scripts | \\
--	(cd "$install_library_dir" ; \$(TAR) -xf -)
-+	(cd "\${DESTDIR}$install_library_dir" ; \$(TAR) -xf -)
- 	-\$(CD) $vmd_library_dir; \$(TAR) -cf - scripts | \\
--	(cd "$install_library_dir" ; \$(TAR) -xf -)
-+	(cd "\${DESTDIR}$install_library_dir" ; \$(TAR) -xf -)
- 	-\$(CD) ..; \$(TAR) -cf - python | \\
--	(cd "$install_library_dir"/scripts ; \$(TAR) -xf -)
-+	(cd "\${DESTDIR}$install_library_dir"/scripts ; \$(TAR) -xf -)
- 	-\$(CD) ..; \$(TAR) -cf - plugins | \\
--	(cd "$install_library_dir" ; \$(TAR) -xf -)
-+	(cd "\${DESTDIR}$install_library_dir" ; \$(TAR) -xf -)
- 	-\$(CD) ..; \$(TAR) -cf - shaders | \\
--	(cd "$install_library_dir" ; \$(TAR) -xf -)
--	-\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir"
-+	(cd "\${DESTDIR}$install_library_dir" ; \$(TAR) -xf -)
-+	-\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "\${DESTDIR}$install_library_dir"
- 	\$(CD) $vmd_bin_dir ; \\
- 	if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\
- 	if [ ! -x "/bin/csh" ]; then \\
-@@ -3044,7 +3044,7 @@
- 		cat $vmd_bin_csh >> run_vmd_tmp ; \\
- 	fi ; \\
- 	chmod +x run_vmd_tmp ; \\
--	\$(COPY) run_vmd_tmp "$install_bin_dir"/$install_name ; \\
-+	\$(COPY) run_vmd_tmp "\${DESTDIR}$install_bin_dir"/$install_name ; \\
- 	\$(DELETE) run_vmd_tmp
- 	\$(ECHO) Make sure "$install_bin_dir"/$install_name is in your path.
- 	\$(ECHO) "VMD installation complete.  Enjoy!"
diff --git a/science/vmd/files/patch-lib_tachyon_unix_Make-arch b/science/vmd/files/patch-lib_tachyon_unix_Make-arch
index aa8049780694..ef1aade136ff 100644
--- a/science/vmd/files/patch-lib_tachyon_unix_Make-arch
+++ b/science/vmd/files/patch-lib_tachyon_unix_Make-arch
@@ -1,6 +1,6 @@
---- Make-arch-orig	Fri Mar 25 14:34:38 2005
-+++ lib/tachyon/unix/Make-arch	Fri Mar 25 14:34:50 2005
-@@ -989,7 +989,7 @@
+--- lib/tachyon/unix/Make-arch.orig	2013-04-21 19:09:28 UTC
++++ lib/tachyon/unix/Make-arch
+@@ -1103,7 +1103,7 @@ bsd:
  	$(MAKE) all \
  	"ARCH = bsd" \
  	"CC = gcc" \
diff --git a/science/vmd/pkg-plist b/science/vmd/pkg-plist
index b725d1b0cc52..418f47aab794 100644
--- a/science/vmd/pkg-plist
+++ b/science/vmd/pkg-plist
@@ -5,7 +5,7 @@ lib/vmd/Announcement
 lib/vmd/LICENSE
 lib/vmd/README
 lib/vmd/doc/ug.pdf
-lib/vmd/plugins/%%VMD_ARCH%%/bin/catdcd4.0/catdcd
+lib/vmd/plugins/%%VMD_ARCH%%/bin/catdcd5.1/catdcd
 lib/vmd/plugins/%%VMD_ARCH%%/bin/cionize1.0/cionize
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/abinitplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/avsplugin.so
@@ -42,6 +42,7 @@ lib/vmd/plugins/%%VMD_ARCH%%/molfile/mapplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/mdfplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/mol2plugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/moldenplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/molemeshplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/msmsplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/namdbinplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/offplugin.so
@@ -49,8 +50,10 @@ lib/vmd/plugins/%%VMD_ARCH%%/molfile/parm7plugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/parmplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/pbeqplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/pdbplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/pdbxplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/phiplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/pltplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/plyplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/pqrplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/psfplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/raster3dplugin.so
@@ -60,6 +63,7 @@ lib/vmd/plugins/%%VMD_ARCH%%/molfile/spiderplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/stlplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/tinkerplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/uhbdplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/vasp5xdatcarplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspchgcarplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspoutcarplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspparchgplugin.so
@@ -67,77 +71,66 @@ lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspposcarplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspxdatcarplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspxmlplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/vtfplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/vtkplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/webpdbplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/xbgfplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/xsfplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/xyzplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.3/psfcheck.so
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.3/pkgIndex.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.3/autopsf.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/cionize1.0/pkgIndex.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.6/autopsf.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.6/pkgIndex.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.6/psfcheck.so
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/bossconvert1.0/Topology
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/bossconvert1.0/bossconvert.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/bossconvert1.0/imprlist
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/bossconvert1.0/oplsaa.par
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/bossconvert1.0/oplsaa.sb
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/bossconvert1.0/pkgIndex.tcl
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/cionize1.0/cionize.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/cionize1.0/pkgIndex.tcl
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/clustalw1.1/clustalw
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/clustalw1.1/pkgIndex.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/clustalw1.1/clustalw_help
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/clustalw1.1/clustalw.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/clustalw1.1/mafft.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/clustalw1.1/clustalw_help
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/clustalw1.1/pkgIndex.tcl
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/hesstrans1.0/hesstrans.so
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/hesstrans1.0/pkgIndex.tcl
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 lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/libbiokit.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/seqqr
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/structqr
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/libbiokit_entropy.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/libbiokit_profcombine.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/metric.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/percid
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/pkgIndex.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/q
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/qpair
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/rmsd
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/percid
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/seqqr
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/structqr
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/libbiokit1.1/tcl_libbiokit.so
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-lib/vmd/plugins/%%VMD_ARCH%%/tcl/mutator1.4/pkgIndex.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/mutator1.4/mutator_gui.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/mutator1.4/mutator.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/upgmaclu
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/mafft1.1/mafft.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/mafft1.1/pkgIndex.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/mutator1.5/libalchemify.so
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/mutator1.5/mutator.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/mutator1.5/mutator_gui.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/mutator1.5/pkgIndex.tcl
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 lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/pkgIndex.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_widget.tcl
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-lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_newick.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_matrixviewer.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_je.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_export.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_data.tcl
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_analysis.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/cluster.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_data.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_export.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_je.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_matrixviewer.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_newick.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_nexus.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_nodeprops.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/phylotree_widget.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/pkgIndex.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/phylotree1.2/upgmaclu
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0/libpmepot.so
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0/pkgIndex.tcl
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0/pmepot.tcl
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0/pmepot_gui.tcl
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.6/libpsfgen.so
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.6/ug.pdf
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.6/pkgIndex.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/specden.so
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/signalproc.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/fftpack.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/data_io_lib.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/pkgIndex.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/fftcmds.so
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/sgsmooth.so
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/stamp
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/stamp.defaults
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/pdb.directories
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/dssp.directories
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/pkgIndex.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/stamp.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/rnaview
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/pkgIndex.tcl
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-lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/CVS/Root
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/CVS/Repository
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/CVS/Entries
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.6/ug.pdf
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/Atomic_A.pdb
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/Atomic_C.pdb
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/Atomic_G.pdb
@@ -145,16 +138,39 @@ lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/Atomic_I.pdb
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/Atomic_P.pdb
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/Atomic_T.pdb
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/Atomic_U.pdb
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/CVS/Entries
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/CVS/Repository
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/CVS/Root
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/misc_rna.par
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/ps_image.par
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/raster3d.par
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/vrml_image.par
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/volutil1.3/volutil
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/pkgIndex.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/rnaview
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/rnaview.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/data_io_lib.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/fftcmds.so
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/fftpack.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/pkgIndex.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/sgsmooth.so
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/signalproc.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/signalproc1.1/specden.so
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/dssp.directories
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/pdb.directories
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/pkgIndex.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/stamp
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/stamp.defaults
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/stamp1.2/stamp.tcl
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/volutil1.3/pkgIndex.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/volutil1.3/volutil
 lib/vmd/plugins/%%VMD_ARCH%%/tcl/volutil1.3/volutil.tcl
 lib/vmd/plugins/include/molfile_plugin.h
 lib/vmd/plugins/include/vmdconio.h
 lib/vmd/plugins/include/vmdplugin.h
+lib/vmd/plugins/noarch/tcl/alascanfep1.0/alascan.tcl
+lib/vmd/plugins/noarch/tcl/alascanfep1.0/alascan_analysis.tcl
+lib/vmd/plugins/noarch/tcl/alascanfep1.0/fep.tcl
+lib/vmd/plugins/noarch/tcl/alascanfep1.0/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/apbsrun1.3/apbsrun.tcl
 lib/vmd/plugins/noarch/tcl/apbsrun1.3/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/apbsrun1.3/radii.dat
@@ -168,9 +184,38 @@ lib/vmd/plugins/noarch/tcl/autoimd1.7/autoimd.tcl
 lib/vmd/plugins/noarch/tcl/autoimd1.7/namdrun.tcl
 lib/vmd/plugins/noarch/tcl/autoimd1.7/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/autoimd1.7/ug.pdf
-lib/vmd/plugins/noarch/tcl/autoionize1.3/autoionize.tcl
-lib/vmd/plugins/noarch/tcl/autoionize1.3/autoionizegui.tcl
-lib/vmd/plugins/noarch/tcl/autoionize1.3/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/autoionize1.4/autoionize.tcl
+lib/vmd/plugins/noarch/tcl/autoionize1.4/autoionizegui.tcl
+lib/vmd/plugins/noarch/tcl/autoionize1.4/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/bdtk1.0/bdtk.tcl
+lib/vmd/plugins/noarch/tcl/bdtk1.0/bdtk_gui.tcl
+lib/vmd/plugins/noarch/tcl/bdtk1.0/bdtk_procs.tcl
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/CVS/Entries
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/CVS/Repository
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/CVS/Root
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/interactions.dat
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/ions.dat
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/membrane.dat
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/potentials/CVS/Entries
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/potentials/CVS/Repository
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/potentials/CVS/Root
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/potentials/extend114_chl-chl.dat
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/potentials/extend114_pot-chl.dat
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/potentials/extend114_pot-pot.dat
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/potentials/graphene_cla.dat
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/potentials/graphene_pot.dat
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/shapes/CVS/Entries
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/shapes/CVS/Repository
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/shapes/CVS/Root
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/shapes/shape1.gif
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/shapes/shape1.shp
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/shapes/shape2.gif
+lib/vmd/plugins/noarch/tcl/bdtk1.0/database/shapes/shape2.shp
+lib/vmd/plugins/noarch/tcl/bdtk1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/bendix1.1/GUI-tips.gif
+lib/vmd/plugins/noarch/tcl/bendix1.1/Monsieur_Bendix_smaller_still.gif
+lib/vmd/plugins/noarch/tcl/bendix1.1/bendix.tcl
+lib/vmd/plugins/noarch/tcl/bendix1.1/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/bignum1.0/bignum.tcl
 lib/vmd/plugins/noarch/tcl/bignum1.0/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/biocore1.1/biocore.tcl
@@ -182,29 +227,29 @@ lib/vmd/plugins/noarch/tcl/biocore1.1/biocoreutil.tcl
 lib/vmd/plugins/noarch/tcl/biocore1.1/locked.gif
 lib/vmd/plugins/noarch/tcl/biocore1.1/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/biocore1.1/unlocked.gif
-lib/vmd/plugins/noarch/tcl/blast1.1/blast.tcl
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-lib/vmd/plugins/noarch/tcl/cgtools1.0/rbcg-2007.top
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-lib/vmd/plugins/noarch/tcl/chirality1.1/chirality.tcl
-lib/vmd/plugins/noarch/tcl/cispeptide1.1/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/cispeptide1.1/cispeptide_gui.tcl
-lib/vmd/plugins/noarch/tcl/cispeptide1.1/cispeptide.tcl
+lib/vmd/plugins/noarch/tcl/blast1.11/blast.tcl
+lib/vmd/plugins/noarch/tcl/blast1.11/blast_resultviewer.tcl
+lib/vmd/plugins/noarch/tcl/blast1.11/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.2/cggui.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.2/cgnetworking.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.2/cgtools.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.2/protein.cgc
+lib/vmd/plugins/noarch/tcl/cgtools1.2/rbcg-2007.par
+lib/vmd/plugins/noarch/tcl/cgtools1.2/rbcg-2007.top
+lib/vmd/plugins/noarch/tcl/cgtools1.2/water.cgc
+lib/vmd/plugins/noarch/tcl/chirality1.2/chirality.tcl
+lib/vmd/plugins/noarch/tcl/chirality1.2/chirality_gui.tcl
+lib/vmd/plugins/noarch/tcl/chirality1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/cispeptide1.3/cispeptide.tcl
+lib/vmd/plugins/noarch/tcl/cispeptide1.3/cispeptide_gui.tcl
+lib/vmd/plugins/noarch/tcl/cispeptide1.3/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/cliptool1.0/cliptool.tcl
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-lib/vmd/plugins/noarch/tcl/colorscalebar1.3/colorscalebar.tcl
-lib/vmd/plugins/noarch/tcl/colorscalebar1.3/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/clonerep1.3/clonerep.tcl
+lib/vmd/plugins/noarch/tcl/clonerep1.3/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/colorscalebar1.4/colorscalebar.tcl
+lib/vmd/plugins/noarch/tcl/colorscalebar1.4/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/contactmap1.1/contactmap.tcl
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@@ -221,40 +266,41 @@ lib/vmd/plugins/noarch/tcl/exectool1.2/jobmanager.tcl
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+lib/vmd/plugins/noarch/tcl/fftk1.1/fftk.tcl
+lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_BondAngleOpt.tcl
+lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_BuildPar.tcl
+lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_ChargeOpt.tcl
+lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_DihOpt.tcl
+lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_GenBonded.tcl
+lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_GenDihScan.tcl
+lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_GenZMatrix.tcl
+lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_GeomOpt.tcl
+lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_SharedFcns.tcl
+lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_distort.tcl
+lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_guiInterface.tcl
+lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_guiProcs.tcl
+lib/vmd/plugins/noarch/tcl/fftk1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/gofrgui1.3/gofrgui.tcl
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+lib/vmd/plugins/noarch/tcl/heatmapper1.1/heatmapper.tcl
+lib/vmd/plugins/noarch/tcl/heatmapper1.1/pkgIndex.tcl
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+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/basemol/water.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/convert_xbgf_to_frags.tcl
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+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/CVS/Repository
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/CVS/Root
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/amino.mfrag
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+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/furan_2C.frag
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+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/methyl.pdb
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/nitrile.frag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/nitro.frag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/fragments/phenyl.mfrag
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+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/C.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/CVS/Entries
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/CVS/Repository
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/CVS/Root
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/G.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/T.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/U.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/dna_backbone.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/dna_dihedrals.gif
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/rna_backbone.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/lib/nucleic_acids/rna_backbone_added.mfrag
+lib/vmd/plugins/noarch/tcl/molefacture1.4/molefacture.tcl
+lib/vmd/plugins/noarch/tcl/molefacture1.4/molefacture_builder.tcl
+lib/vmd/plugins/noarch/tcl/molefacture1.4/molefacture_edit.tcl
+lib/vmd/plugins/noarch/tcl/molefacture1.4/molefacture_geometry.tcl
+lib/vmd/plugins/noarch/tcl/molefacture1.4/molefacture_gui.tcl
+lib/vmd/plugins/noarch/tcl/molefacture1.4/molefacture_internals.tcl
+lib/vmd/plugins/noarch/tcl/molefacture1.4/molefacture_state.tcl
+lib/vmd/plugins/noarch/tcl/molefacture1.4/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/moltoptools0.1/moltoptools.tcl
 lib/vmd/plugins/noarch/tcl/moltoptools0.1/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/multimolanim1.0/multimolanim.tcl
 lib/vmd/plugins/noarch/tcl/multimolanim1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/multiplot1.6/multiplot.tcl
-lib/vmd/plugins/noarch/tcl/multiplot1.6/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/multiplot1.7/multiplot.tcl
+lib/vmd/plugins/noarch/tcl/multiplot1.7/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/multiseq2.1/colormap_vmd.tcl
 lib/vmd/plugins/noarch/tcl/multiseq2.1/export_options.tcl
 lib/vmd/plugins/noarch/tcl/multiseq2.1/find.tcl
@@ -440,36 +489,36 @@ lib/vmd/plugins/noarch/tcl/multiseqdialog1.1/multiseqdialog.tcl
 lib/vmd/plugins/noarch/tcl/multiseqdialog1.1/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/multiseqdialog1.1/scrolledframe.tcl
 lib/vmd/plugins/noarch/tcl/multiseqdialog1.1/wait_dialog.tcl
-lib/vmd/plugins/noarch/tcl/multitext1.0/multitext.tcl
-lib/vmd/plugins/noarch/tcl/multitext1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/multitext1.1/multitext.tcl
+lib/vmd/plugins/noarch/tcl/multitext1.1/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/namdenergy1.4/namdenergy.tcl
 lib/vmd/plugins/noarch/tcl/namdenergy1.4/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/namdgui1.3/namdgui.tcl
 lib/vmd/plugins/noarch/tcl/namdgui1.3/namdgui_tclforces.tcl
 lib/vmd/plugins/noarch/tcl/namdgui1.3/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/namdplot1.1/namdplot.tcl
-lib/vmd/plugins/noarch/tcl/namdplot1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/namdplot1.2/namdplot.tcl
+lib/vmd/plugins/noarch/tcl/namdplot1.2/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/namdserver1.1/namdserver.tcl
 lib/vmd/plugins/noarch/tcl/namdserver1.1/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/nanotube1.2/nanotube.tcl
-lib/vmd/plugins/noarch/tcl/nanotube1.2/graphene.tcl
-lib/vmd/plugins/noarch/tcl/nanotube1.2/gui.tcl
-lib/vmd/plugins/noarch/tcl/nanotube1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/nanotube1.5/graphene.tcl
+lib/vmd/plugins/noarch/tcl/nanotube1.5/gui.tcl
+lib/vmd/plugins/noarch/tcl/nanotube1.5/nanotube.tcl
+lib/vmd/plugins/noarch/tcl/nanotube1.5/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/navfly1.0/navfly.tcl
 lib/vmd/plugins/noarch/tcl/navfly1.0/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/navigate1.0/navigate.tcl
 lib/vmd/plugins/noarch/tcl/navigate1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/networkview1.0/suboptimalPaths.tcl
-lib/vmd/plugins/noarch/tcl/networkview1.0/adjacencyMatrix.tcl
-lib/vmd/plugins/noarch/tcl/networkview1.0/networkSetup.tcl
-lib/vmd/plugins/noarch/tcl/networkview1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/networkview1.0/communityNetwork.tcl
-lib/vmd/plugins/noarch/tcl/networkview1.0/networkViewGui.tcl
-lib/vmd/plugins/noarch/tcl/networkview1.0/networkView.tcl
-lib/vmd/plugins/noarch/tcl/nmwiz1.0/pkgIndex.tcl
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-lib/vmd/plugins/noarch/tcl/optimization1.1/optimization.tcl
-lib/vmd/plugins/noarch/tcl/optimization1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/networkview1.41/adjacencyMatrix.tcl
+lib/vmd/plugins/noarch/tcl/networkview1.41/communityNetwork.tcl
+lib/vmd/plugins/noarch/tcl/networkview1.41/networkSetup.tcl
+lib/vmd/plugins/noarch/tcl/networkview1.41/networkView.tcl
+lib/vmd/plugins/noarch/tcl/networkview1.41/networkViewGui.tcl
+lib/vmd/plugins/noarch/tcl/networkview1.41/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/networkview1.41/suboptimalPaths.tcl
+lib/vmd/plugins/noarch/tcl/nmwiz1.2/nmwiz.tcl
+lib/vmd/plugins/noarch/tcl/nmwiz1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/optimization1.3/optimization.tcl
+lib/vmd/plugins/noarch/tcl/optimization1.3/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/palettetool1.0/palettetool.tcl
 lib/vmd/plugins/noarch/tcl/palettetool1.0/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/paratool1.5/paratool.tcl
@@ -489,20 +538,23 @@ lib/vmd/plugins/noarch/tcl/paratool1.5/paratool_respcharges.tcl
 lib/vmd/plugins/noarch/tcl/paratool1.5/paratool_tmcomplex.tcl
 lib/vmd/plugins/noarch/tcl/paratool1.5/paratool_topology.tcl
 lib/vmd/plugins/noarch/tcl/paratool1.5/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/parsefep1.5/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/parsefep1.5/parseFEP.tcl
-lib/vmd/plugins/noarch/tcl/pbctools2.6/pbcbox.tcl
-lib/vmd/plugins/noarch/tcl/pbctools2.6/pbcgui.tcl
-lib/vmd/plugins/noarch/tcl/pbctools2.6/pbcjoin.tcl
-lib/vmd/plugins/noarch/tcl/pbctools2.6/pbcset.tcl
-lib/vmd/plugins/noarch/tcl/pbctools2.6/pbctools.tcl
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-lib/vmd/plugins/noarch/tcl/pbctools2.6/pbcwrap.tcl
-lib/vmd/plugins/noarch/tcl/pbctools2.6/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/parsefep1.9/parseFEP.tcl
+lib/vmd/plugins/noarch/tcl/parsefep1.9/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/pbctools2.8/pbcbox.tcl
+lib/vmd/plugins/noarch/tcl/pbctools2.8/pbcgui.tcl
+lib/vmd/plugins/noarch/tcl/pbctools2.8/pbcjoin.tcl
+lib/vmd/plugins/noarch/tcl/pbctools2.8/pbcset.tcl
+lib/vmd/plugins/noarch/tcl/pbctools2.8/pbctools.tcl
+lib/vmd/plugins/noarch/tcl/pbctools2.8/pbcunwrap.tcl
+lib/vmd/plugins/noarch/tcl/pbctools2.8/pbcwrap.tcl
+lib/vmd/plugins/noarch/tcl/pbctools2.8/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/pdbtool1.0/pdbtool.tcl
 lib/vmd/plugins/noarch/tcl/pdbtool1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/plumed0.9/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/plumed0.9/vmdplumed.tcl
+lib/vmd/plugins/noarch/tcl/plumed2.5/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/plumed2.5/templates_list_v1.tcl
+lib/vmd/plugins/noarch/tcl/plumed2.5/templates_list_v2.tcl
+lib/vmd/plugins/noarch/tcl/plumed2.5/templates_list_vmdcv.tcl
+lib/vmd/plugins/noarch/tcl/plumed2.5/vmdplumed.tcl
 lib/vmd/plugins/noarch/tcl/propka1.1/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/propka1.1/propka.tcl
 lib/vmd/plugins/noarch/tcl/psipred1.1/pkgIndex.tcl
@@ -516,31 +568,57 @@ lib/vmd/plugins/noarch/tcl/qmtool1.3/qmtool_charges.tcl
 lib/vmd/plugins/noarch/tcl/qmtool1.3/qmtool_intcoor.tcl
 lib/vmd/plugins/noarch/tcl/qmtool1.3/qmtool_readwrite.tcl
 lib/vmd/plugins/noarch/tcl/qmtool1.3/qmtool_setup.tcl
+lib/vmd/plugins/noarch/tcl/qwikmd1.1/Annealing.conf
+lib/vmd/plugins/noarch/tcl/qwikmd1.1/Equilibration.conf
+lib/vmd/plugins/noarch/tcl/qwikmd1.1/MD.conf
+lib/vmd/plugins/noarch/tcl/qwikmd1.1/Minimization.conf
+lib/vmd/plugins/noarch/tcl/qwikmd1.1/SMD.conf
+lib/vmd/plugins/noarch/tcl/qwikmd1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/qwikmd1.1/qwikmd.tcl
+lib/vmd/plugins/noarch/tcl/qwikmd1.1/qwikmd_ballon.tcl
+lib/vmd/plugins/noarch/tcl/qwikmd1.1/qwikmd_func.tcl
+lib/vmd/plugins/noarch/tcl/qwikmd1.1/qwikmd_info.tcl
+lib/vmd/plugins/noarch/tcl/qwikmd1.1/qwikmd_logText.tcl
 lib/vmd/plugins/noarch/tcl/ramaplot1.1/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/ramaplot1.1/ramaplot.tcl
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-lib/vmd/plugins/noarch/tcl/readcharmmpar1.2/par_all36_lipid.prm
-lib/vmd/plugins/noarch/tcl/readcharmmpar1.2/par_amber2charmm.inp
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-lib/vmd/plugins/noarch/tcl/readcharmmtop1.1/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/readcharmmtop1.1/readcharmmtop.tcl
-lib/vmd/plugins/noarch/tcl/readcharmmtop1.1/top_all27_hybrid.inp
-lib/vmd/plugins/noarch/tcl/readcharmmtop1.1/top_all27_prot_lipid_na.inp
-lib/vmd/plugins/noarch/tcl/readcharmmtop1.1/top_all36_lipid.rtf
-lib/vmd/plugins/noarch/tcl/readcharmmtop1.1/top_amber2charmm.inp
-lib/vmd/plugins/noarch/tcl/remote0.1/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/remote0.1/remote.tcl
+lib/vmd/plugins/noarch/tcl/readcharmmpar1.3/par_all22_prot.prm
+lib/vmd/plugins/noarch/tcl/readcharmmpar1.3/par_all27_prot_lipid_na.inp
+lib/vmd/plugins/noarch/tcl/readcharmmpar1.3/par_all36_carb.prm
+lib/vmd/plugins/noarch/tcl/readcharmmpar1.3/par_all36_cgenff.prm
+lib/vmd/plugins/noarch/tcl/readcharmmpar1.3/par_all36_lipid.prm
+lib/vmd/plugins/noarch/tcl/readcharmmpar1.3/par_all36_na.prm
+lib/vmd/plugins/noarch/tcl/readcharmmpar1.3/par_all36_prot.prm
+lib/vmd/plugins/noarch/tcl/readcharmmpar1.3/par_amber2charmm.inp
+lib/vmd/plugins/noarch/tcl/readcharmmpar1.3/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/readcharmmpar1.3/readcharmmpar.tcl
+lib/vmd/plugins/noarch/tcl/readcharmmpar1.3/toppar_all36_carb_glycopeptide.str
+lib/vmd/plugins/noarch/tcl/readcharmmpar1.3/toppar_water_ions_namd.str
+lib/vmd/plugins/noarch/tcl/readcharmmtop1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/readcharmmtop1.2/readcharmmtop.tcl
+lib/vmd/plugins/noarch/tcl/readcharmmtop1.2/top_all22_prot.rtf
+lib/vmd/plugins/noarch/tcl/readcharmmtop1.2/top_all27_hybrid.inp
+lib/vmd/plugins/noarch/tcl/readcharmmtop1.2/top_all27_prot_lipid_na.inp
+lib/vmd/plugins/noarch/tcl/readcharmmtop1.2/top_all36_carb.rtf
+lib/vmd/plugins/noarch/tcl/readcharmmtop1.2/top_all36_cgenff.rtf
+lib/vmd/plugins/noarch/tcl/readcharmmtop1.2/top_all36_hybrid.inp
+lib/vmd/plugins/noarch/tcl/readcharmmtop1.2/top_all36_lipid.rtf
+lib/vmd/plugins/noarch/tcl/readcharmmtop1.2/top_all36_na.rtf
+lib/vmd/plugins/noarch/tcl/readcharmmtop1.2/top_all36_prot.rtf
+lib/vmd/plugins/noarch/tcl/readcharmmtop1.2/top_amber2charmm.inp
+lib/vmd/plugins/noarch/tcl/readcharmmtop1.2/toppar_all36_carb_glycopeptide.str
+lib/vmd/plugins/noarch/tcl/readcharmmtop1.2/toppar_water_ions_namd.str
+lib/vmd/plugins/noarch/tcl/remote0.6/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/remote0.6/remote.tcl
 lib/vmd/plugins/noarch/tcl/resptool1.2/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/resptool1.2/resptool.tcl
 lib/vmd/plugins/noarch/tcl/rmsd1.0/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/rmsd1.0/rmsd.tcl
 lib/vmd/plugins/noarch/tcl/rmsdtt3.0/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/rmsdtt3.0/rmsdtt.tcl
+lib/vmd/plugins/noarch/tcl/rmsdvt1.0/modal.tcl
 lib/vmd/plugins/noarch/tcl/rmsdvt1.0/pkgIndex.tcl
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 lib/vmd/plugins/noarch/tcl/rmsdvt1.0/rmsdvt-gui.tcl
-lib/vmd/plugins/noarch/tcl/rmsdvt1.0/modal.tcl
+lib/vmd/plugins/noarch/tcl/rmsdvt1.0/rmsdvt.tcl
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 lib/vmd/plugins/noarch/tcl/ruler1.0/ruler.tcl
 lib/vmd/plugins/noarch/tcl/runante0.2/pkgIndex.tcl
@@ -608,36 +686,75 @@ lib/vmd/plugins/noarch/tcl/seqedit1.1/seqedit_widget_edit.tcl
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 lib/vmd/plugins/noarch/tcl/seqedit1.1/seqedit_widget_statusbar.tcl
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-lib/vmd/plugins/noarch/tcl/solvate1.5/wat.top
+lib/vmd/plugins/noarch/tcl/solvate1.7/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/solvate1.7/solvate.tcl
+lib/vmd/plugins/noarch/tcl/solvate1.7/wat.pdb
+lib/vmd/plugins/noarch/tcl/solvate1.7/wat.psf
+lib/vmd/plugins/noarch/tcl/solvate1.7/wat.top
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 lib/vmd/plugins/noarch/tcl/stingtool1.0/stingtool.tcl
+lib/vmd/plugins/noarch/tcl/structurecheck1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/structurecheck1.1/structurecheck.tcl
 lib/vmd/plugins/noarch/tcl/symmetrytool1.3/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/symmetrytool1.3/symmetry.tcl
+lib/vmd/plugins/noarch/tcl/tablelist5.13/CHANGES.txt
+lib/vmd/plugins/noarch/tcl/tablelist5.13/COPYRIGHT.txt
+lib/vmd/plugins/noarch/tcl/tablelist5.13/README.txt
+lib/vmd/plugins/noarch/tcl/tablelist5.13/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/tablelist5.13/scripts/mwutil.tcl
+lib/vmd/plugins/noarch/tcl/tablelist5.13/scripts/pencil.cur
+lib/vmd/plugins/noarch/tcl/tablelist5.13/scripts/repair.tcl
+lib/vmd/plugins/noarch/tcl/tablelist5.13/scripts/tablelistBind.tcl
+lib/vmd/plugins/noarch/tcl/tablelist5.13/scripts/tablelistConfig.tcl
+lib/vmd/plugins/noarch/tcl/tablelist5.13/scripts/tablelistEdit.tcl
+lib/vmd/plugins/noarch/tcl/tablelist5.13/scripts/tablelistImages.tcl
+lib/vmd/plugins/noarch/tcl/tablelist5.13/scripts/tablelistMove.tcl
+lib/vmd/plugins/noarch/tcl/tablelist5.13/scripts/tablelistSort.tcl
+lib/vmd/plugins/noarch/tcl/tablelist5.13/scripts/tablelistThemes.tcl
+lib/vmd/plugins/noarch/tcl/tablelist5.13/scripts/tablelistUtil.tcl
+lib/vmd/plugins/noarch/tcl/tablelist5.13/scripts/tablelistWidget.tcl
+lib/vmd/plugins/noarch/tcl/tablelist5.13/scripts/tclIndex
+lib/vmd/plugins/noarch/tcl/tablelist5.13/tablelist.tcl
+lib/vmd/plugins/noarch/tcl/tablelist5.13/tablelistPublic.tcl
+lib/vmd/plugins/noarch/tcl/tablelist5.13/tablelist_tile.tcl
 lib/vmd/plugins/noarch/tcl/timeline2.3/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/timeline2.3/timeline.tcl
-lib/vmd/plugins/noarch/tcl/topotools1.2/README
-lib/vmd/plugins/noarch/tcl/topotools1.2/par_CG.prm
-lib/vmd/plugins/noarch/tcl/topotools1.2/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/topotools1.2/top_CG.prm
-lib/vmd/plugins/noarch/tcl/topotools1.2/topoangles.tcl
-lib/vmd/plugins/noarch/tcl/topotools1.2/topoatoms.tcl
-lib/vmd/plugins/noarch/tcl/topotools1.2/topobonds.tcl
-lib/vmd/plugins/noarch/tcl/topotools1.2/topocgcmm.tcl
-lib/vmd/plugins/noarch/tcl/topotools1.2/topodihedrals.tcl
-lib/vmd/plugins/noarch/tcl/topotools1.2/topogromacs.tcl
-lib/vmd/plugins/noarch/tcl/topotools1.2/topohelpers.tcl
-lib/vmd/plugins/noarch/tcl/topotools1.2/topoimpropers.tcl
-lib/vmd/plugins/noarch/tcl/topotools1.2/topolammps.tcl
-lib/vmd/plugins/noarch/tcl/topotools1.2/topotools.tcl
-lib/vmd/plugins/noarch/tcl/topotools1.2/topoutils.tcl
-lib/vmd/plugins/noarch/tcl/topotools1.2/topovarxyz.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.7/README
+lib/vmd/plugins/noarch/tcl/topotools1.7/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.7/topoangles.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.7/topoatoms.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.7/topobonds.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.7/topocrossterms.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.7/topodihedrals.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.7/topogromacs.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.7/topohelpers.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.7/topoimpropers.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.7/topolammps.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.7/topotools.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.7/topoutils.tcl
+lib/vmd/plugins/noarch/tcl/topotools1.7/topovarxyz.tcl
+lib/vmd/plugins/noarch/tcl/torsionplot1.1/AMAN_12_AMAN.dx
+lib/vmd/plugins/noarch/tcl/torsionplot1.1/AMAN_12_BGLN.dx
+lib/vmd/plugins/noarch/tcl/torsionplot1.1/AMAN_14_BGLN.dx
+lib/vmd/plugins/noarch/tcl/torsionplot1.1/AMAN_16_AMAN.dx
+lib/vmd/plugins/noarch/tcl/torsionplot1.1/BGLN_14_BMAN.dx
+lib/vmd/plugins/noarch/tcl/torsionplot1.1/BGLN_16_AFUC.dx
+lib/vmd/plugins/noarch/tcl/torsionplot1.1/BGLN_or_AMAN_14_BGLN.dx
+lib/vmd/plugins/noarch/tcl/torsionplot1.1/BMAN_16_AMAN.dx
+lib/vmd/plugins/noarch/tcl/torsionplot1.1/MAN_13_AMAN.dx
+lib/vmd/plugins/noarch/tcl/torsionplot1.1/NGLB_FUC.dx
+lib/vmd/plugins/noarch/tcl/torsionplot1.1/NGLB_no_FUC.dx
+lib/vmd/plugins/noarch/tcl/torsionplot1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/torsionplot1.1/rama-cispro.dx
+lib/vmd/plugins/noarch/tcl/torsionplot1.1/rama-general.dx
+lib/vmd/plugins/noarch/tcl/torsionplot1.1/rama-gly.dx
+lib/vmd/plugins/noarch/tcl/torsionplot1.1/rama-ileval.dx
+lib/vmd/plugins/noarch/tcl/torsionplot1.1/rama-prepro-noGP.dx
+lib/vmd/plugins/noarch/tcl/torsionplot1.1/rama-transpro.dx
+lib/vmd/plugins/noarch/tcl/torsionplot1.1/torsionplot.tcl
 lib/vmd/plugins/noarch/tcl/trunctraj1.5/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/trunctraj1.5/toppar/acepar19.inp
 lib/vmd/plugins/noarch/tcl/trunctraj1.5/toppar/acepar22_prot.inp
@@ -692,20 +809,41 @@ lib/vmd/plugins/noarch/tcl/trunctraj1.5/toppar/top_all30_cheq_prot.inp
 lib/vmd/plugins/noarch/tcl/trunctraj1.5/toppar/toph19.inp
 lib/vmd/plugins/noarch/tcl/trunctraj1.5/toppar/toprna10r_22.inp
 lib/vmd/plugins/noarch/tcl/trunctraj1.5/trunctraj.tcl
-lib/vmd/plugins/noarch/tcl/utilities1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/utilities1.0/utilities.tcl
+lib/vmd/plugins/noarch/tcl/utilities1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/utilities1.2/utilities.tcl
 lib/vmd/plugins/noarch/tcl/vdna2.2/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/vdna2.2/vdna.tcl
-lib/vmd/plugins/noarch/tcl/viewchangerender1.6/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/viewchangerender1.6/vcr_gui.tcl
-lib/vmd/plugins/noarch/tcl/viewchangerender1.6/vcr.tcl
-lib/vmd/plugins/noarch/tcl/viewmaster2.5/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/viewmaster2.5/viewmaster.tcl
-lib/vmd/plugins/noarch/tcl/vmddebug1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/vmddebug1.0/debugatomsel.tcl
-lib/vmd/plugins/noarch/tcl/vmddebug1.0/vmddebug.tcl
+lib/vmd/plugins/noarch/tcl/viewchangerender1.8/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/viewchangerender1.8/vcr.tcl
+lib/vmd/plugins/noarch/tcl/viewchangerender1.8/vcr_gui.tcl
+lib/vmd/plugins/noarch/tcl/viewmaster2.6/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/viewmaster2.6/viewmaster.tcl
+lib/vmd/plugins/noarch/tcl/vmddebug1.1/debugatomsel.tcl
+lib/vmd/plugins/noarch/tcl/vmddebug1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/vmddebug1.1/vmddebug.tcl
+lib/vmd/plugins/noarch/tcl/vmdlite1.1/centerMolecule.tcl
+lib/vmd/plugins/noarch/tcl/vmdlite1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/vmdlite1.1/sandboxMolecules/1nqg.pdb
+lib/vmd/plugins/noarch/tcl/vmdlite1.1/sandboxMolecules/1ubq.pdb
+lib/vmd/plugins/noarch/tcl/vmdlite1.1/sandboxMolecules/3zoj.pdb
+lib/vmd/plugins/noarch/tcl/vmdlite1.1/sandboxMolecules/6tna.pdb
+lib/vmd/plugins/noarch/tcl/vmdlite1.1/sandboxMolecules/CVS/Entries
+lib/vmd/plugins/noarch/tcl/vmdlite1.1/sandboxMolecules/CVS/Repository
+lib/vmd/plugins/noarch/tcl/vmdlite1.1/sandboxMolecules/CVS/Root
+lib/vmd/plugins/noarch/tcl/vmdlite1.1/sandboxMolecules/bdna.pdb
+lib/vmd/plugins/noarch/tcl/vmdlite1.1/sandboxMolecules/membrane.pdb
+lib/vmd/plugins/noarch/tcl/vmdlite1.1/vmd.rc
+lib/vmd/plugins/noarch/tcl/vmdlite1.1/vmdlite.tcl
+lib/vmd/plugins/noarch/tcl/vmdlite1.1/vmdlite_analysis.tcl
+lib/vmd/plugins/noarch/tcl/vmdlite1.1/vmdlite_graphics.tcl
+lib/vmd/plugins/noarch/tcl/vmdlite1.1/vmdlite_guiProcs.tcl
+lib/vmd/plugins/noarch/tcl/vmdlite1.1/vmdlite_main.tcl
+lib/vmd/plugins/noarch/tcl/vmdlite1.1/vmdlite_sandbox.tcl
+lib/vmd/plugins/noarch/tcl/vmdlite1.1/vmdlite_system.tcl
 lib/vmd/plugins/noarch/tcl/vmdmovie1.9/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/vmdmovie1.9/vmdmovie.tcl
+lib/vmd/plugins/noarch/tcl/vmdprefs1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/vmdprefs1.0/vmdprefs.tcl
 lib/vmd/plugins/noarch/tcl/vmdtkcon1.1/README
 lib/vmd/plugins/noarch/tcl/vmdtkcon1.1/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/vmdtkcon1.1/tkcon-2.3/CVS/Entries
@@ -740,8 +878,8 @@ lib/vmd/plugins/noarch/tcl/vmdtkcon1.1/tkcon-modified.tcl
 lib/vmd/plugins/noarch/tcl/vmdtkcon1.1/vmdtkcon.tcl
 lib/vmd/plugins/noarch/tcl/volmapgui1.1/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/volmapgui1.1/volmapgui.tcl
-lib/vmd/plugins/noarch/tcl/zoomseq1.1/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/zoomseq1.1/zoomseq.tcl
+lib/vmd/plugins/noarch/tcl/zoomseq1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/zoomseq1.2/zoomseq.tcl
 lib/vmd/scripts/CVS/Entries
 lib/vmd/scripts/CVS/Repository
 lib/vmd/scripts/CVS/Root
@@ -1173,9 +1311,9 @@ lib/vmd/shaders/CVS/Root
 lib/vmd/shaders/vmd.frag
 lib/vmd/shaders/vmd.vert
 lib/vmd/shaders/vmdsphere.frag
+lib/vmd/shaders/vmdsphere.vert
 lib/vmd/shaders/vmdspheresprite.frag
 lib/vmd/shaders/vmdspheresprite.vert
-lib/vmd/shaders/vmdsphere.vert
 lib/vmd/stride_%%VMD_ARCH%%
 lib/vmd/surf_%%VMD_ARCH%%
 lib/vmd/tachyon_%%VMD_ARCH%%