9 files changed, 354 insertions, 261 deletions

diff --git a/science/vmd/Makefile b/science/vmd/Makefile
index 87d95062236a..00d250fc0f5c 100644
--- a/science/vmd/Makefile
+++ b/science/vmd/Makefile
@@ -6,10 +6,10 @@
 #
 
 PORTNAME=		vmd
-PORTVERSION=		1.8.2
-PORTREVISION=		2
+PORTVERSION=		1.8.3
+PORTREVISION=		0
 CATEGORIES=		science graphics python tcl84 tk84
-MASTER_SITES=		http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.96/ \
+MASTER_SITES=		http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.97/ \
 			ftp://ftp.ebi.ac.uk/pub/software/unix/stride/src/
 DISTFILES=		${VMD_DIST} ${TACHYON_DIST} ${STRIDE_DIST}
 
@@ -33,7 +33,7 @@ NO_CDROM=		"License has restrictions"
 RESTRICTED=		"License has restrictions"
 
 VMD_DIST=		${PORTNAME}-${PORTVERSION}.src.tar.gz
-TACHYON_DIST=		tachyon-0.96.tar.gz
+TACHYON_DIST=		tachyon-0.97.tar.gz
 STRIDE_DIST=		stride.tar.gz
 
 .include <bsd.port.pre.mk>
@@ -63,10 +63,10 @@ ${VMD_DIST}.  Please place this file in ${DISTDIR}.\n
 
 do-extract:
 	${MKDIR} ${WRKDIR}
-	cd ${WRKDIR} && ${TAR} xfz ${DISTDIR}/${VMD_DIST}
-	cd ${WRKSRC}/lib/surf && ${TAR} xfz surf.tar.Z
-	cd ${WRKSRC}/lib && ${TAR} xfz ${DISTDIR}/${TACHYON_DIST}
-	cd ${WRKSRC}/lib/stride && ${TAR} xfz ${DISTDIR}/${STRIDE_DIST}
+	${TAR} xfz ${DISTDIR}/${VMD_DIST} -C ${WRKDIR}
+	${TAR} xfz ${WRKSRC}/lib/surf/surf.tar.Z -C ${WRKSRC}/lib/surf
+	${TAR} xfz ${DISTDIR}/${TACHYON_DIST} -C ${WRKSRC}/lib
+	${TAR} xfz ${DISTDIR}/${STRIDE_DIST} -C ${WRKSRC}/lib/stride
 
 post-patch:
 	${REINPLACE_CMD} "s/-lpthread/${PTHREAD_LIBS}/" ${WRKSRC}/configure
@@ -74,17 +74,19 @@ post-patch:
 	${REINPLACE_CMD} "s/-ltcl8.4/-ltcl84/" ${WRKSRC}/configure
 	${REINPLACE_CMD} "s%\$$python_dir/lib_\$$config_arch%${PREFIX}%" ${WRKSRC}/configure
 	${REINPLACE_CMD} "s/python2.2/${PYTHON_VERSION}/" ${WRKSRC}/configure
+	${REINPLACE_CMD} "s/.SILENT:/#.SILENT:/" ${WRKDIR}/plugins/Makefile
+	${REINPLACE_CMD} "s/.SILENT:/#.SILENT:/" ${WRKDIR}/plugins/*/Makefile
 
 do-build:
-	cd ${WRKSRC}/lib/tachyon/unix && ${SETENV} ${MAKE_ENV} ${GMAKE} bsd && ${MV} ../compile/bsd/tachyon ../tachyon_${VMD_ARCH}
-	cd ${WRKDIR}/plugins && ${SETENV} ${MAKE_ENV} PLUGINDIR=${WRKSRC}/plugins ${GMAKE} ${VMD_ARCH} distrib
-	cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} TCL_INCLUDE_DIR=${PREFIX}/include/tcl8.4 TK_INCLUDE_DIR=${PREFIX}/include/tk8.4 ${GMAKE} ${VMD_TARGET}
-	cd ${WRKSRC}/src && ${SETENV} ${MAKE_ENV} ${GMAKE} all
-	cd ${WRKSRC}/lib/surf && ${SETENV} ${MAKE_ENV} ${GMAKE} depend && ${SETENV} ${MAKE_ENV} ${GMAKE} surf && ${MV} surf surf_${VMD_ARCH}
-	cd ${WRKSRC}/lib/stride && ${SETENV} ${MAKE_ENV} ${GMAKE} && ${MV} stride stride_${VMD_ARCH}
+	${SETENV} ${MAKE_ENV} ${GMAKE} bsd -C ${WRKSRC}/lib/tachyon/unix && ${MV} ${WRKSRC}/lib/tachyon/compile/bsd/tachyon ${WRKSRC}/lib/tachyon/tachyon_${VMD_ARCH}
+	${SETENV} ${MAKE_ENV} PLUGINDIR=${WRKSRC}/plugins ${GMAKE} ${VMD_ARCH} distrib -C ${WRKDIR}/plugins
+	${SETENV} ${MAKE_ENV} TCL_INCLUDE_DIR=${PREFIX}/include/tcl8.4 TK_INCLUDE_DIR=${PREFIX}/include/tk8.4 ${GMAKE} ${VMD_TARGET} -C ${WRKSRC}
+	${SETENV} ${MAKE_ENV} ${GMAKE} all -C ${WRKSRC}/src
+	${SETENV} ${MAKE_ENV} ${GMAKE} depend -C ${WRKSRC}/lib/surf && ${SETENV} ${MAKE_ENV} ${GMAKE} surf -C ${WRKSRC}/lib/surf && ${MV} ${WRKSRC}/lib/surf/surf ${WRKSRC}/lib/surf/surf_${VMD_ARCH}
+	${SETENV} ${MAKE_ENV} ${GMAKE} -C ${WRKSRC}/lib/stride && ${MV} ${WRKSRC}/lib/stride/stride ${WRKSRC}/lib/stride/stride_${VMD_ARCH}
 
 do-install:
-	cd ${WRKSRC}/src && ${SETENV} ${MAKE_ENV} ${GMAKE} install
-#	cd ${WRKSRC}/lib/surf && ${INSTALL_PROGRAM} surf_${VMD_ARCH} ${PREFIX}/lib/vmd
+	${SETENV} ${MAKE_ENV} ${GMAKE} -C ${WRKSRC}/src install
+	@${CHOWN} -R ${SHAREOWN}:${SHAREGRP} ${PREFIX}/lib/vmd
 
 .include <bsd.port.post.mk>
diff --git a/science/vmd/distinfo b/science/vmd/distinfo
index 24df7f7013f8..d98d34e7fce8 100644
--- a/science/vmd/distinfo
+++ b/science/vmd/distinfo
@@ -1,6 +1,6 @@
-MD5 (vmd-1.8.2.src.tar.gz) = 8ad9cb90d954740f3b54be585526698d
-SIZE (vmd-1.8.2.src.tar.gz) = 7192878
-MD5 (tachyon-0.96.tar.gz) = db695196231a304b8102c1d6a0f6f6f2
-SIZE (tachyon-0.96.tar.gz) = 2419955
+MD5 (vmd-1.8.3.src.tar.gz) = 8fb3fa55a54bcc3e41dbbd53c1c2cc59
+SIZE (vmd-1.8.3.src.tar.gz) = 8590337
+MD5 (tachyon-0.97.tar.gz) = 198953aea283a7158eef2ee079e909f6
+SIZE (tachyon-0.97.tar.gz) = 2485223
 MD5 (stride.tar.gz) = bdef3a3e1af8cbdf8fbfefacfa9a929f
 SIZE (stride.tar.gz) = 56441
diff --git a/science/vmd/files/patch-Make-arch b/science/vmd/files/patch-Make-arch
index b2e6ed661726..f476206f9363 100644
--- a/science/vmd/files/patch-Make-arch
+++ b/science/vmd/files/patch-Make-arch
@@ -1,5 +1,5 @@
---- ../plugins/Make-arch.orig	Fri Nov 14 07:50:25 2003
-+++ ../plugins/Make-arch	Fri Jan 21 19:30:53 2005
+--- Make-arch.orig	Mon Feb  7 13:09:55 2005
++++ ../plugins/Make-arch	Fri Mar 25 16:54:01 2005
 @@ -9,6 +9,7 @@
  	@echo "--------------------------------------"
  	@echo " AIX4"
@@ -8,10 +8,14 @@
  	@echo " HPUX11"
  	@echo " IRIX6"
  	@echo " IRIX6_64"
-@@ -142,6 +143,20 @@
+@@ -142,8 +143,22 @@
+ 	"LOPTO = -o " \
+ 	"CC = gcc" \
  	"CXX = g++" \
- 	"CCFLAGS = -O2 -Wall -ansi -I/usr/local/include/tcl8.4" \
- 	"CXXFLAGS = -O2 -Wall" \
+-	"CCFLAGS = -O2 -Wall -I/usr/local/include/tcl8.4" \
+-	"CXXFLAGS = -O2 -Wall" \
++	"CCFLAGS = ${CFLAGS} -O2 -Wall -I/usr/local/include/tcl8.4" \
++	"CXXFLAGS = ${CFLAGS} -O2 -Wall" \
 +	"TCLLDFLAGS = -L/usr/local/lib -ltcl84" \
 +	"NM = nm -p" \
 +	"RANLIB = touch" \
@@ -24,8 +28,8 @@
 +	"LOPTO = -fPIC -m64 -o " \
 +	"CC = gcc" \
 +	"CXX = g++" \
-+	"CCFLAGS = -m64 -O2 -Wall -ansi -I/usr/local/include/tcl8.4" \
-+	"CXXFLAGS = -m64 -O2 -Wall" \
++	"CCFLAGS = ${CFLAGS} -m64 -O2 -Wall -I/usr/local/include/tcl8.4" \
++	"CXXFLAGS = ${CFLAGS} -m64 -O2 -Wall" \
  	"TCLLDFLAGS = -L/usr/local/lib -ltcl84" \
  	"NM = nm -p" \
  	"RANLIB = touch" \
diff --git a/science/vmd/files/patch-Makefile b/science/vmd/files/patch-Makefile
index c8bd108b6b52..59ad76f3cc4e 100644
--- a/science/vmd/files/patch-Makefile
+++ b/science/vmd/files/patch-Makefile
@@ -5,12 +5,12 @@
  ## FreeBSD builds
  freebsd.mesa:
 -	./configure FREEBSD MESA FLTK TK TCL IMD VRPN PYTHON PTHREADS LIBTACHYON NUMPY SILENT
-+	./configure FREEBSD MESA FLTK TK TCL IMD PYTHON PTHREADS LIBTACHYON NUMPY SILENT
++	./configure FREEBSD MESA FLTK TK TCL IMD PYTHON PTHREADS LIBTACHYON NUMPY
  
  # FreeBSD doesn't have hardware good accelleration support
  freebsd.opengl:
 -	./configure FREEBSD OPENGL FLTK TK IMD VRPN SILENT SPACEBALL TCL PTHREADS ACTC LIBTACHYON PYTHON NUMPY
-+	./configure FREEBSD OPENGL FLTK TK IMD SILENT TCL PTHREADS LIBTACHYON PYTHON NUMPY
++	./configure FREEBSD OPENGL FLTK TK IMD TCL PTHREADS LIBTACHYON PYTHON NUMPY
 +
 +freebsd.amd64.opengl:
 +	./configure FREEBSDAMD64 OPENGL FLTK TK IMD SILENT TCL PTHREADS LIBTACHYON PYTHON NUMPY
diff --git a/science/vmd/files/patch-configure b/science/vmd/files/patch-configure
index 252ed252c42f..72a717480095 100644
--- a/science/vmd/files/patch-configure
+++ b/science/vmd/files/patch-configure
@@ -109,3 +109,17 @@
   
      if ($config_python) {
        # this is to make python happy
+@@ -2052,11 +2114,11 @@
+ 
+ # compiler and compiler directives 
+ CC          = $arch_cc
+-CFLAGS      = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
+ COMPILERC   = $arch_compilerc
+ RCFLAGS     = $arch_rcflags
+ CCPP	    = $arch_ccpp
+-CPPFLAGS    = $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
++CPPFLAGS    = \${CXXFLAGS} $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
++CFLAGS      += $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
+ 
+ DEPEND      = $arch_depend_flag
+ DEPENDFILE  = Makedata.depend
diff --git a/science/vmd/files/patch-lib_tachyon_unix_Make-arch b/science/vmd/files/patch-lib_tachyon_unix_Make-arch
new file mode 100644
index 000000000000..2d67afb4b77c
--- /dev/null
+++ b/science/vmd/files/patch-lib_tachyon_unix_Make-arch
@@ -0,0 +1,11 @@
+--- Make-arch-orig	Fri Mar 25 14:34:38 2005
++++ lib/tachyon/unix/Make-arch	Fri Mar 25 14:34:50 2005
+@@ -859,7 +859,7 @@
+ 	$(MAKE) all \
+ 	"ARCH = bsd" \
+ 	"CC = gcc" \
+-	"CFLAGS = -O6 -fomit-frame-pointer -ffast-math -DBsd  $(MISCFLAGS)" \
++	"CFLAGS += -O6 -fomit-frame-pointer -ffast-math -DBsd  $(MISCFLAGS)" \
+ 	"AR = ar" \
+ 	"ARFLAGS = r" \
+ 	"STRIP = strip" \
diff --git a/science/vmd/files/patch-stride_Makefile b/science/vmd/files/patch-stride_Makefile
new file mode 100644
index 000000000000..e3fab512fd07
--- /dev/null
+++ b/science/vmd/files/patch-stride_Makefile
@@ -0,0 +1,10 @@
+--- lib/stride/Makefile-orig	Fri Mar 25 17:51:11 2005
++++ lib/stride/Makefile	Fri Mar 25 17:49:22 2005
+@@ -1,6 +1,6 @@
+ #CC = gcc -O2  # ->> for DJGPP compiler under DOS and for SunOS; also suitable for other machines
+ 
+-CC = cc -O2
++CC = cc ${CFLAGS} -O2
+ FLAGS = -lm  -o
+ 
+ SOURCE = stride.c splitstr.c rdpdb.c initchn.c geometry.c thr2one.c one2thr.c filename.c tolostr.c strutil.c place_h.c hbenergy.c memory.c helix.c sheet.c rdmap.c phipsi.c command.c molscr.c die.c hydrbond.c mergepat.c fillasn.c escape.c p_jrnl.c p_rem.c p_atom.c p_helix.c p_sheet.c p_turn.c p_ssbond.c p_expdta.c p_model.c p_compnd.c report.c nsc.c area.c ssbond.c chk_res.c chk_atom.c turn.c pdbasn.c dssp.c outseq.c chkchain.c elem.c measure.c asngener.c p_endmdl.c stred.c
diff --git a/science/vmd/files/patch-surf_Makefile b/science/vmd/files/patch-surf_Makefile
new file mode 100644
index 000000000000..f8136f812ce7
--- /dev/null
+++ b/science/vmd/files/patch-surf_Makefile
@@ -0,0 +1,11 @@
+--- lib/surf/Makefile.orig	Fri Mar 25 17:52:40 2005
++++ lib/surf/Makefile	Fri Mar 25 17:50:20 2005
+@@ -6,7 +6,7 @@
+ LINCLUDE    = -lm
+ OPT_CFLAGS  = -O2 $(FLAGS) $(INCLUDE)
+ #CFLAGS	    = -g $(FLAGS) $(INCLUDE)
+-CFLAGS	    = -O2 $(FLAGS) $(INCLUDE)
++CFLAGS	    += -O2 $(FLAGS) $(INCLUDE)
+ 
+ # These are the user object files in the application
+ SRCS        = surf.c io.c compute.c dual.c utils.c lp.c chull.c tessel_cases.c \
diff --git a/science/vmd/pkg-plist b/science/vmd/pkg-plist
index 6018c05ac527..b78504ff706c 100644
--- a/science/vmd/pkg-plist
+++ b/science/vmd/pkg-plist
@@ -1,40 +1,164 @@
 bin/vmd
-lib/vmd/doc/ug.pdf
 lib/vmd/Announcement
-lib/vmd/README
 lib/vmd/LICENSE
-lib/vmd/vmd_%%VMD_ARCH%%
-lib/vmd/surf_%%VMD_ARCH%%
-lib/vmd/stride_%%VMD_ARCH%%
-lib/vmd/tachyon_%%VMD_ARCH%%
-lib/vmd/scripts/CVS/Root
-lib/vmd/scripts/CVS/Repository
+lib/vmd/README
+lib/vmd/.vmdrc
+lib/vmd/.vmdsensors
+lib/vmd/doc/ug.pdf
+lib/vmd/plugins/%%VMD_ARCH%%/bin/catdcd4.0/catdcd
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/avsplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/babelplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/binposplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/brixplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/carplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/ccp4plugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/corplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/cpmdplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/crdplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/cubeplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/dcdplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/dlpolyplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/dsn6plugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/dxplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/edmplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/fs4plugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/gamessplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/graspplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/grdplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/gridplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/gromacsplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/lammpsplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/libmolfile_plugin.a
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/libmolfile_plugin.h
+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/namdbinplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/parm7plugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/parmplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/pdbplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/phiplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/pltplugin.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
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/rst7plugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/stlplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/tinkerplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/webpdbplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/xsfplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/xyzplugin.so
+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/psfgen1.3/libpsfgen.so
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.3/pkgIndex.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.3/ug.pdf
+lib/vmd/plugins/include/molfile_plugin.h
+lib/vmd/plugins/include/vmdplugin.h
+lib/vmd/plugins/noarch/tcl/apbsrun1.0/apbsrun.tcl
+lib/vmd/plugins/noarch/tcl/apbsrun1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/apbsrun1.0/radii.dat
+lib/vmd/plugins/noarch/tcl/autoimd1.4/autoimd-api.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.4/autoimd-gui.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.4/autoimd-settings.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.4/autoimd-template.namd
+lib/vmd/plugins/noarch/tcl/autoimd1.4/autoimd.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.4/namdrun.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.4/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.4/ug.pdf
+lib/vmd/plugins/noarch/tcl/autoionize1.1/autoionize.tcl
+lib/vmd/plugins/noarch/tcl/autoionize1.1/ions.top
+lib/vmd/plugins/noarch/tcl/autoionize1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/cliptool1.0/cliptool.tcl
+lib/vmd/plugins/noarch/tcl/cliptool1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/contactmap1.1/contactmap.tcl
+lib/vmd/plugins/noarch/tcl/contactmap1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/exectool1.0/exectool.tcl
+lib/vmd/plugins/noarch/tcl/exectool1.0/jobmanager.tcl
+lib/vmd/plugins/noarch/tcl/exectool1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/imdmenu1.0/imdmenu.tcl
+lib/vmd/plugins/noarch/tcl/imdmenu1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/membrane1.0/membrane.tcl
+lib/vmd/plugins/noarch/tcl/membrane1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/membrane1.0/popc_box.pdb
+lib/vmd/plugins/noarch/tcl/membrane1.0/popc_box.psf
+lib/vmd/plugins/noarch/tcl/membrane1.0/pope_box.pdb
+lib/vmd/plugins/noarch/tcl/membrane1.0/pope_box.psf
+lib/vmd/plugins/noarch/tcl/membrane1.0/top_all27_prot_lipid.inp
+lib/vmd/plugins/noarch/tcl/navigate1.0/navigate.tcl
+lib/vmd/plugins/noarch/tcl/navigate1.0/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/ramaplot1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/ramaplot1.0/ramaplot.tcl
+lib/vmd/plugins/noarch/tcl/rmsd1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/rmsd1.0/rmsd.tcl
+lib/vmd/plugins/noarch/tcl/solvate1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/solvate1.2/solvate.tcl
+lib/vmd/plugins/noarch/tcl/solvate1.2/wat.pdb
+lib/vmd/plugins/noarch/tcl/solvate1.2/wat.psf
+lib/vmd/plugins/noarch/tcl/solvate1.2/wat.top
+lib/vmd/plugins/noarch/tcl/timeline1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/timeline1.0/timeline.tcl
+lib/vmd/plugins/noarch/tcl/viewmaster2.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/viewmaster2.1/viewmaster.tcl
+lib/vmd/plugins/noarch/tcl/vmdmovie1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/vmdmovie1.2/vmdmovie.tcl
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/README
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/CVS/Entries
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/CVS/Repository
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/CVS/Root
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/ChangeLog
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/README.txt
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/CVS/Entries
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/CVS/Repository
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/CVS/Root
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/bindings.html
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/changes.txt
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/demopic.gif
+lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/docs/dump.html
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+lib/vmd/scripts/tk8.4/entry.tcl
+lib/vmd/scripts/tk8.4/focus.tcl
+lib/vmd/scripts/tk8.4/images/README
+lib/vmd/scripts/tk8.4/images/logo.eps
+lib/vmd/scripts/tk8.4/images/logo100.gif
+lib/vmd/scripts/tk8.4/images/logo64.gif
+lib/vmd/scripts/tk8.4/images/logoLarge.gif
+lib/vmd/scripts/tk8.4/images/logoMed.gif
+lib/vmd/scripts/tk8.4/images/pwrdLogo.eps
+lib/vmd/scripts/tk8.4/images/pwrdLogo100.gif
+lib/vmd/scripts/tk8.4/images/pwrdLogo150.gif
+lib/vmd/scripts/tk8.4/images/pwrdLogo175.gif
+lib/vmd/scripts/tk8.4/images/pwrdLogo200.gif
+lib/vmd/scripts/tk8.4/images/pwrdLogo75.gif
+lib/vmd/scripts/tk8.4/images/tai-ku.gif
+lib/vmd/scripts/tk8.4/listbox.tcl
+lib/vmd/scripts/tk8.4/menu.tcl
+lib/vmd/scripts/tk8.4/mkpsenc.tcl
+lib/vmd/scripts/tk8.4/msgbox.tcl
+lib/vmd/scripts/tk8.4/msgs/cs.msg
+lib/vmd/scripts/tk8.4/msgs/de.msg
+lib/vmd/scripts/tk8.4/msgs/el.msg
+lib/vmd/scripts/tk8.4/msgs/en.msg
+lib/vmd/scripts/tk8.4/msgs/en_gb.msg
+lib/vmd/scripts/tk8.4/msgs/es.msg
+lib/vmd/scripts/tk8.4/msgs/fr.msg
+lib/vmd/scripts/tk8.4/msgs/it.msg
+lib/vmd/scripts/tk8.4/msgs/nl.msg
+lib/vmd/scripts/tk8.4/msgs/ru.msg
+lib/vmd/scripts/tk8.4/obsolete.tcl
+lib/vmd/scripts/tk8.4/optMenu.tcl
+lib/vmd/scripts/tk8.4/palette.tcl
+lib/vmd/scripts/tk8.4/panedwindow.tcl
+lib/vmd/scripts/tk8.4/prolog.ps
+lib/vmd/scripts/tk8.4/safetk.tcl
+lib/vmd/scripts/tk8.4/scale.tcl
+lib/vmd/scripts/tk8.4/scrlbar.tcl
+lib/vmd/scripts/tk8.4/spinbox.tcl
+lib/vmd/scripts/tk8.4/tclIndex
+lib/vmd/scripts/tk8.4/tearoff.tcl
+lib/vmd/scripts/tk8.4/text.tcl
+lib/vmd/scripts/tk8.4/tk.tcl
+lib/vmd/scripts/tk8.4/tkAppInit.c
+lib/vmd/scripts/tk8.4/tkfbox.tcl
+lib/vmd/scripts/tk8.4/unsupported.tcl
+lib/vmd/scripts/tk8.4/xmfbox.tcl
+lib/vmd/scripts/vmd/CVS/Entries
+lib/vmd/scripts/vmd/CVS/Repository
+lib/vmd/scripts/vmd/CVS/Root
+lib/vmd/scripts/vmd/README.chemical2vmd
+lib/vmd/scripts/vmd/atomselect.tcl
+lib/vmd/scripts/vmd/atomselmacros.tcl
+lib/vmd/scripts/vmd/biocore.tcl
+lib/vmd/scripts/vmd/chemical2vmd
+lib/vmd/scripts/vmd/colordefs.dat
+lib/vmd/scripts/vmd/draw.tcl
+lib/vmd/scripts/vmd/graphlabels.tcl
+lib/vmd/scripts/vmd/hotkeys.tcl
+lib/vmd/scripts/vmd/logfile.tcl
+lib/vmd/scripts/vmd/openURL.tcl
+lib/vmd/scripts/vmd/restypes.dat
+lib/vmd/scripts/vmd/save_state.tcl
+lib/vmd/scripts/vmd/tclIndex
+lib/vmd/scripts/vmd/vectors.tcl
+lib/vmd/scripts/vmd/vmdinit.tcl
+lib/vmd/scripts/vmd/www.tcl
+lib/vmd/shaders/CVS/Entries
+lib/vmd/shaders/CVS/Repository
+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/stride_%%VMD_ARCH%%
+lib/vmd/surf_%%VMD_ARCH%%
+lib/vmd/tachyon_%%VMD_ARCH%%
+lib/vmd/vmd_%%VMD_ARCH%%
+@dirrm lib/vmd/shaders/CVS
+@dirrm lib/vmd/shaders
 @dirrm lib/vmd/scripts/vmd/CVS
 @dirrm lib/vmd/scripts/vmd
 @dirrm lib/vmd/scripts/tk8.4/msgs
@@ -393,24 +429,29 @@ lib/vmd/scripts/tk8.0
 @dirrm lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3/CVS
 @dirrm lib/vmd/plugins/noarch/tcl/vmdtkcon1.0/tkcon-2.3
 @dirrm lib/vmd/plugins/noarch/tcl/vmdtkcon1.0
-@dirrm lib/vmd/plugins/noarch/tcl/vmdmovie1.1
+@dirrm lib/vmd/plugins/noarch/tcl/vmdmovie1.2
+@dirrm lib/vmd/plugins/noarch/tcl/viewmaster2.1
 @dirrm lib/vmd/plugins/noarch/tcl/timeline1.0
 @dirrm lib/vmd/plugins/noarch/tcl/solvate1.2
 @dirrm lib/vmd/plugins/noarch/tcl/rmsd1.0
 @dirrm lib/vmd/plugins/noarch/tcl/ramaplot1.0
 @dirrm lib/vmd/plugins/noarch/tcl/pdbtool1.0
-@dirrm lib/vmd/plugins/noarch/tcl/namdrun0.1
+@dirrm lib/vmd/plugins/noarch/tcl/navigate1.0
 @dirrm lib/vmd/plugins/noarch/tcl/membrane1.0
-@dirrm lib/vmd/plugins/noarch/tcl/jmvexport1.0
 @dirrm lib/vmd/plugins/noarch/tcl/imdmenu1.0
-@dirrm lib/vmd/plugins/noarch/tcl/contactmap1.0
-@dirrm lib/vmd/plugins/noarch/tcl/autoionize1.0
-@dirrm lib/vmd/plugins/noarch/tcl/autoimd1.3
-@dirrm lib/vmd/plugins/noarch/tcl/aligntool1.0
+@dirrm lib/vmd/plugins/noarch/tcl/exectool1.0
+@dirrm lib/vmd/plugins/noarch/tcl/contactmap1.1
+@dirrm lib/vmd/plugins/noarch/tcl/cliptool1.0
+@dirrm lib/vmd/plugins/noarch/tcl/autoionize1.1
+@dirrm lib/vmd/plugins/noarch/tcl/autoimd1.4
+@dirrm lib/vmd/plugins/noarch/tcl/apbsrun1.0
 @dirrm lib/vmd/plugins/noarch/tcl
 @dirrm lib/vmd/plugins/noarch
 @dirrm lib/vmd/plugins/include
+@dirrm lib/vmd/plugins/%%VMD_ARCH%%/bin/catdcd4.0
+@dirrm lib/vmd/plugins/%%VMD_ARCH%%/bin
 @dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.3
+@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0
 @dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl
 @dirrm lib/vmd/plugins/%%VMD_ARCH%%/molfile
 @dirrm lib/vmd/plugins/%%VMD_ARCH%%