path: root/sci-chemistry/vmd/files/vmd-1.8.7-gentoo.patch

diff --git a/plugins/Makefile b/plugins/Makefile
index e2e5e5e..f2eabaf 100755
--- a/plugins/Makefile
+++ b/plugins/Makefile
@@ -4,7 +4,6 @@
 ## Theoretical and Computational Biophysics Group
 ##
 
-.SILENT:
 
 default: make-arch-help
 
diff --git a/plugins/Makefile.newmultiseq b/plugins/Makefile.newmultiseq
index c271b44..d00522c 100644
--- a/plugins/Makefile.newmultiseq
+++ b/plugins/Makefile.newmultiseq
@@ -4,7 +4,6 @@
 ## Theoretical and Computational Biophysics Group
 ##
 
-.SILENT:
 
 default: make-arch-help
 
diff --git a/plugins/Makefile.orig b/plugins/Makefile.orig
index e6406fd..6208576 100644
--- a/plugins/Makefile.orig
+++ b/plugins/Makefile.orig
@@ -4,7 +4,6 @@
 ## Theoretical and Computational Biophysics Group
 ##
 
-.SILENT:
 
 default: make-arch-help
 
diff --git a/plugins/Makefile.rej b/plugins/Makefile.rej
index 1b6ea67..d13aca1 100644
--- a/plugins/Makefile.rej
+++ b/plugins/Makefile.rej
@@ -3,7 +3,6 @@
   # Makefile for molecule file readers
   # $Id: vmd-1.8.7-gentoo.patch,v 1.2 2010/07/27 18:47:33 jlec Exp $
   
-- .SILENT:
   
   .SUFFIXES:
   
@@ -17,7 +16,6 @@
   # Makefile for molecule file readers
   # $Id: vmd-1.8.7-gentoo.patch,v 1.2 2010/07/27 18:47:33 jlec Exp $
   
-+ .SILENT:
   
   .SUFFIXES:
   
diff --git a/plugins/aligntool/Makefile b/plugins/aligntool/Makefile
index 8155a6d..e4df74c 100644
--- a/plugins/aligntool/Makefile
+++ b/plugins/aligntool/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = aligntool.tcl cealign.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/apbsrun/Makefile b/plugins/apbsrun/Makefile
index aca0b4e..b86ee59 100644
--- a/plugins/apbsrun/Makefile
+++ b/plugins/apbsrun/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = apbsrun.tcl pkgIndex.tcl radii.dat
 VMVERSION = 1.3
diff --git a/plugins/atomedit/Makefile b/plugins/atomedit/Makefile
index 558606c..05d7f90 100644
--- a/plugins/atomedit/Makefile
+++ b/plugins/atomedit/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = atomedit.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/autoimd/Makefile b/plugins/autoimd/Makefile
index 9d432e4..7f0a802 100644
--- a/plugins/autoimd/Makefile
+++ b/plugins/autoimd/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 AUTOIMDFILES = autoimd.tcl autoimd-settings.tcl autoimd-api.tcl autoimd-gui.tcl pkgIndex.tcl autoimd-template.namd doc/ug.pdf namdrun.tcl
 AUTOIMDVERSION = 1.6
diff --git a/plugins/autoionize/Makefile b/plugins/autoionize/Makefile
index c74ad01..b392d3f 100644
--- a/plugins/autoionize/Makefile
+++ b/plugins/autoionize/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = autoionize.tcl autoionizegui.tcl pkgIndex.tcl ions.top
 VMVERSION = 1.2
diff --git a/plugins/bignum/Makefile b/plugins/bignum/Makefile
index 9c90f17..c35322d 100644
--- a/plugins/bignum/Makefile
+++ b/plugins/bignum/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = bignum.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/biocore/Makefile b/plugins/biocore/Makefile
index 887b592..d2919dd 100644
--- a/plugins/biocore/Makefile
+++ b/plugins/biocore/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = biocore.tcl biocorechat.tcl biocorelogin.tcl biocorepubsync.tcl pkgIndex.tcl locked.gif unlocked.gif biocoreHelper.tcl biocoreutil.tcl
 
diff --git a/plugins/catdcd/Makefile b/plugins/catdcd/Makefile
index 7a8f0f8..bbc4c01 100644
--- a/plugins/catdcd/Makefile
+++ b/plugins/catdcd/Makefile
@@ -1,6 +1,5 @@
 # Makefile for catdcd
 
-.SILENT:
 
 .SUFFIXES: 
 
@@ -45,8 +44,8 @@ ${ARCHDIR}/catdcd.exe : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfi
 	LINK ${CATDCDOBJS} /OUT:${ARCHDIR}/catdcd.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS}
 
 # all other platforms
-${ARCHDIR}/catdcd : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a
-	${CXX} ${CXXFLAGS} ${CATDCDOBJS} -o ${ARCHDIR}/catdcd -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm
+${ARCHDIR}/catdcd : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.h
+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${CATDCDOBJS} -o ${ARCHDIR}/catdcd -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm
 
 ${ARCHDIR}/hash.o: hash.h hash.c
 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o
diff --git a/plugins/cgtools/Makefile b/plugins/cgtools/Makefile
index adca18b..84bf723 100644
--- a/plugins/cgtools/Makefile
+++ b/plugins/cgtools/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = cggui.tcl cgtools.tcl cgnetworking.tcl pkgIndex.tcl \
           protein.cgc water.cgc rbcg-2007.par rbcg-2007.top
diff --git a/plugins/cionize/.#Makefile.specialbuilds.1.1 b/plugins/cionize/.#Makefile.specialbuilds.1.1
index 4672932..181ba85 100644
--- a/plugins/cionize/.#Makefile.specialbuilds.1.1
+++ b/plugins/cionize/.#Makefile.specialbuilds.1.1
@@ -1,6 +1,5 @@
 # Makefile for cionize
 
-#.SILENT:
 
 .SUFFIXES: 
 
diff --git a/plugins/cionize/Makefile b/plugins/cionize/Makefile
index c5fe136..b72116f 100644
--- a/plugins/cionize/Makefile
+++ b/plugins/cionize/Makefile
@@ -1,6 +1,5 @@
 # Makefile for cionize
 
-#.SILENT:
 
 .SUFFIXES: 
 
@@ -52,8 +51,8 @@ ${ARCHDIR}/cionize.exe : ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPI
 	LINK ${IONIZEOBJS} ${MGPOTOBJS} /OUT:${ARCHDIR}/cionize.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS}
 
 # all other platforms
-${ARCHDIR}/cionize: ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a
-	${CXX} ${CXXFLAGS} ${ARCHDIR}/cionize.o ${IONIZEOBJS} ${MGPOTOBJS} -o ${ARCHDIR}/cionize -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm
+${ARCHDIR}/cionize: ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.h
+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/cionize.o ${IONIZEOBJS} ${MGPOTOBJS} -o ${ARCHDIR}/cionize -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} -lm
 
 ${ARCHDIR}/hash.o: hash.h hash.c
 	${CC}  ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o
diff --git a/plugins/cionize/Makefile.mine b/plugins/cionize/Makefile.mine
index 5ee841a..1588837 100644
--- a/plugins/cionize/Makefile.mine
+++ b/plugins/cionize/Makefile.mine
@@ -1,6 +1,5 @@
 # Makefile for cionize
 
-#.SILENT:
 
 .SUFFIXES: 
 
diff --git a/plugins/cionize/Makefile.mine.old b/plugins/cionize/Makefile.mine.old
index 48714b6..0dc4085 100644
--- a/plugins/cionize/Makefile.mine.old
+++ b/plugins/cionize/Makefile.mine.old
@@ -1,6 +1,5 @@
 # Makefile for cionize
 
-#.SILENT:
 
 .SUFFIXES: 
 
diff --git a/plugins/cionize/Makefile.specialbuilds b/plugins/cionize/Makefile.specialbuilds
index a529758..f85bcfe 100644
--- a/plugins/cionize/Makefile.specialbuilds
+++ b/plugins/cionize/Makefile.specialbuilds
@@ -1,6 +1,5 @@
 # Makefile for cionize
 
-#.SILENT:
 
 .SUFFIXES: 
 
diff --git a/plugins/cionize/mcudahacks/Makefile.specialbuilds b/plugins/cionize/mcudahacks/Makefile.specialbuilds
index e93cad2..dc7b632 100644
--- a/plugins/cionize/mcudahacks/Makefile.specialbuilds
+++ b/plugins/cionize/mcudahacks/Makefile.specialbuilds
@@ -1,6 +1,5 @@
 # Makefile for cionize
 
-#.SILENT:
 
 .SUFFIXES: 
 
diff --git a/plugins/cliptool/Makefile b/plugins/cliptool/Makefile
index 9c41370..679abbe 100644
--- a/plugins/cliptool/Makefile
+++ b/plugins/cliptool/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = cliptool.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/clonerep/Makefile b/plugins/clonerep/Makefile
index e8a4949..e101e56 100755
--- a/plugins/clonerep/Makefile
+++ b/plugins/clonerep/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = clonerep.tcl pkgIndex.tcl
 VMVERSION = 1.1
diff --git a/plugins/clustalw/Makefile b/plugins/clustalw/Makefile
index 6329f64..c343b1c 100644
--- a/plugins/clustalw/Makefile
+++ b/plugins/clustalw/Makefile
@@ -1,6 +1,5 @@
 # Makefile for clustalw
 
-.SILENT:
 
 .SUFFIXES: 
 
@@ -66,7 +65,7 @@ OBJS = ${ARCHDIR}/alnscore.o \
 ${ARCHDIR}/clustalw.exe: ${OBJS}
 	LINK ${OBJS} /OUT:${ARCHDIR}/clustalw.exe
 ${ARCHDIR}/clustalw: ${OBJS}
-	${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/clustalw -lm
+	${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/clustalw -lm
     
     
 # Objects.
diff --git a/plugins/cluster/Makefile b/plugins/cluster/Makefile
index 99d347e..dc542f1 100644
--- a/plugins/cluster/Makefile
+++ b/plugins/cluster/Makefile
@@ -1,6 +1,5 @@
 # Makefile for psfgen
 
-.SILENT:
 
 .SUFFIXES: 
 
@@ -48,7 +47,7 @@ ${ARCHDIR}/cluster.exe : ${OBJS}
 
 # all other platforms
 ${ARCHDIR}/cluster : ${OBJS}
-	${CXX} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/cluster -lm
+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/cluster -lm
 
 ${ARCHDIR}/cluster.o: ${SRCDIR}/cluster.c
 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/cluster.c $(COPTO)${ARCHDIR}/cluster.o
diff --git a/plugins/colorscalebar/Makefile b/plugins/colorscalebar/Makefile
index 1413898..f58074a 100644
--- a/plugins/colorscalebar/Makefile
+++ b/plugins/colorscalebar/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = colorscalebar.tcl pkgIndex.tcl
 VMVERSION = 1.2
diff --git a/plugins/contactmap/Makefile b/plugins/contactmap/Makefile
index 36f6b18..3336e41 100644
--- a/plugins/contactmap/Makefile
+++ b/plugins/contactmap/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = contactmap.tcl pkgIndex.tcl
 VMVERSION = 1.1
diff --git a/plugins/dataimport/Makefile b/plugins/dataimport/Makefile
index e63ebca..71b59fb 100644
--- a/plugins/dataimport/Makefile
+++ b/plugins/dataimport/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = dataimport.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/demomaster/Makefile b/plugins/demomaster/Makefile
index 6264d76..27a3d20 100644
--- a/plugins/demomaster/Makefile
+++ b/plugins/demomaster/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = demomaster.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/dipwatch/Makefile b/plugins/dipwatch/Makefile
index 7d36042..4af35c7 100755
--- a/plugins/dipwatch/Makefile
+++ b/plugins/dipwatch/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = dipwatch.tcl pkgIndex.tcl
 VMVERSION = 1.2
diff --git a/plugins/doc/Makefile b/plugins/doc/Makefile
index ed1ce9d..07ff534 100644
--- a/plugins/doc/Makefile
+++ b/plugins/doc/Makefile
@@ -1,7 +1,6 @@
 #
 # Plugin documentation Makefile
 #
-.SILENT:
 
 ECHO            = echo
 DELETEDIR       = rm -rf
diff --git a/plugins/dowser/Makefile b/plugins/dowser/Makefile
index 1795db3..d00cacc 100644
--- a/plugins/dowser/Makefile
+++ b/plugins/dowser/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = dowser.tcl dowser_gui.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/exectool/Makefile b/plugins/exectool/Makefile
index afa024d..6ba1889 100644
--- a/plugins/exectool/Makefile
+++ b/plugins/exectool/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = exectool.tcl jobmanager.tcl pkgIndex.tcl
 VMVERSION = 1.2
diff --git a/plugins/extendedpdb/Makefile b/plugins/extendedpdb/Makefile
index 9061aa1..5a5fb8f 100644
--- a/plugins/extendedpdb/Makefile
+++ b/plugins/extendedpdb/Makefile
@@ -1,4 +1,3 @@
-#.SILENT:
 
 VMFILES = extendedpdb.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/fmtool/Makefile b/plugins/fmtool/Makefile
index 76a9e69..a3f320d 100644
--- a/plugins/fmtool/Makefile
+++ b/plugins/fmtool/Makefile
@@ -1,6 +1,5 @@
 # Makefile for fmtool
 
-.SILENT:
 
 .SUFFIXES: 
 
diff --git a/plugins/gofrgui/Makefile b/plugins/gofrgui/Makefile
index e192f02..7251884 100644
--- a/plugins/gofrgui/Makefile
+++ b/plugins/gofrgui/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = gofrgui.tcl pkgIndex.tcl
 VMVERSION = 1.1
diff --git a/plugins/hbonds/Makefile b/plugins/hbonds/Makefile
index 6bee92d..45f1fe3 100644
--- a/plugins/hbonds/Makefile
+++ b/plugins/hbonds/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = hbonds.tcl pkgIndex.tcl
 VMVERSION = 1.1
diff --git a/plugins/idatm/Makefile b/plugins/idatm/Makefile
index e23ca1c..4280b6a 100644
--- a/plugins/idatm/Makefile
+++ b/plugins/idatm/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = idatm.tcl pkgIndex.tcl
 VMVERSION = 0.1
diff --git a/plugins/ilstools/Makefile b/plugins/ilstools/Makefile
index e145c30..7cc9d1b 100644
--- a/plugins/ilstools/Makefile
+++ b/plugins/ilstools/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 COPYFILES = ilstools.tcl pkgIndex.tcl oxygen.xyz nitricoxide.xyz \
             carbonmonoxide.xyz carbondioxide.xyz ethene.xyz methane.xyz \
diff --git a/plugins/imdmenu/Makefile b/plugins/imdmenu/Makefile
index dca0e25..277f386 100644
--- a/plugins/imdmenu/Makefile
+++ b/plugins/imdmenu/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 IMDMENUFILES = imdmenu.tcl pkgIndex.tcl
 IMDMENUVERSION = 1.0
diff --git a/plugins/inorganicbuilder/Makefile b/plugins/inorganicbuilder/Makefile
index 8e0439a..4af2b0f 100755
--- a/plugins/inorganicbuilder/Makefile
+++ b/plugins/inorganicbuilder/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = inorganicbuilder.tcl pkgIndex.tcl
 VMVERSION = 0.1
diff --git a/plugins/irspecgui/Makefile b/plugins/irspecgui/Makefile
index 754ebc8..e86b09a 100755
--- a/plugins/irspecgui/Makefile
+++ b/plugins/irspecgui/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = irspecgui.tcl pkgIndex.tcl
 VMVERSION = 1.1
diff --git a/plugins/jmvexport/Makefile b/plugins/jmvexport/Makefile
index 7f45260..9eb996b 100644
--- a/plugins/jmvexport/Makefile
+++ b/plugins/jmvexport/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = jmvexport.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/libbiokit/Makefile b/plugins/libbiokit/Makefile
index 7a66d08..12e1fd3 100644
--- a/plugins/libbiokit/Makefile
+++ b/plugins/libbiokit/Makefile
@@ -1,6 +1,5 @@
 # Makefile for libbiokit
 
-.SILENT:
 
 .SUFFIXES: 
 
@@ -111,7 +110,7 @@ ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp : ${INTERFACESRCDIR}/tcl_libbiokit.i
 ${ARCHDIR}/percid.exe: ${ARCHDIR}/percid.o ${OBJS}
 	LINK ${ARCHDIR}/percid.o ${OBJS} /OUT:${ARCHDIR}/percid.exe
 ${ARCHDIR}/percid: ${ARCHDIR}/percid.o ${OBJS}
-	${CXX} ${CXXFLAGS} ${ARCHDIR}/percid.o ${OBJS} -o ${ARCHDIR}/percid -lm
+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/percid.o ${OBJS} -o ${ARCHDIR}/percid -lm
 ${ARCHDIR}/percid.o: ${UTILSRCDIR}/percid.cpp
 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/percid.cpp $(COPTO)${ARCHDIR}/percid.o
 
@@ -119,7 +118,7 @@ ${ARCHDIR}/percid.o: ${UTILSRCDIR}/percid.cpp
 ${ARCHDIR}/qpair.exe: ${ARCHDIR}/qPair.o ${OBJS}
 	LINK ${ARCHDIR}/qPair.o ${OBJS} /OUT:${ARCHDIR}/qpair.exe
 ${ARCHDIR}/qpair: ${ARCHDIR}/qPair.o ${OBJS}
-	${CXX} ${CXXFLAGS} ${ARCHDIR}/qPair.o ${OBJS} -o ${ARCHDIR}/qpair -lm
+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/qPair.o ${OBJS} -o ${ARCHDIR}/qpair -lm
 ${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair.cpp
 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/qPair.cpp $(COPTO)${ARCHDIR}/qPair.o
 
@@ -127,7 +126,7 @@ ${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair.cpp
 ${ARCHDIR}/rmsd.exe: ${ARCHDIR}/rmsd.o ${OBJS}
 	LINK ${ARCHDIR}/rmsd.o ${OBJS} /OUT:${ARCHDIR}/rmsd.exe
 ${ARCHDIR}/rmsd: ${ARCHDIR}/rmsd.o ${OBJS}
-	${CXX} ${CXXFLAGS} ${ARCHDIR}/rmsd.o ${OBJS} -o ${ARCHDIR}/rmsd -lm
+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/rmsd.o ${OBJS} -o ${ARCHDIR}/rmsd -lm
 ${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cpp
 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/rmsd.cpp $(COPTO)${ARCHDIR}/rmsd.o
 
@@ -135,7 +134,7 @@ ${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cpp
 ${ARCHDIR}/q.exe: ${ARCHDIR}/Q.o ${OBJS}
 	LINK ${ARCHDIR}/Q.o ${OBJS} /OUT:${ARCHDIR}/q.exe
 ${ARCHDIR}/q: ${ARCHDIR}/Q.o ${OBJS}
-	${CXX} ${CXXFLAGS} ${ARCHDIR}/Q.o ${OBJS} -o ${ARCHDIR}/q -lm
+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/Q.o ${OBJS} -o ${ARCHDIR}/q -lm
 ${ARCHDIR}/Q.o: ${UTILSRCDIR}/Q.cpp
 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/Q.cpp $(COPTO)${ARCHDIR}/Q.o
 
@@ -143,7 +142,7 @@ ${ARCHDIR}/Q.o: ${UTILSRCDIR}/Q.cpp
 ${ARCHDIR}/seqqr.exe: ${ARCHDIR}/seqqr.o ${OBJS}
 	LINK ${ARCHDIR}/seqqr.o ${OBJS} /OUT:${ARCHDIR}/seqqr.exe
 ${ARCHDIR}/seqqr: ${ARCHDIR}/seqqr.o ${OBJS}
-	${CXX} ${CXXFLAGS} ${ARCHDIR}/seqqr.o ${OBJS} -o ${ARCHDIR}/seqqr -lm
+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/seqqr.o ${OBJS} -o ${ARCHDIR}/seqqr -lm
 ${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr.cpp
 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/seqqr.cpp $(COPTO)${ARCHDIR}/seqqr.o
 
@@ -151,7 +150,7 @@ ${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr.cpp
 ${ARCHDIR}/structqr.exe : ${ARCHDIR}/structqr.o ${OBJS}
 	LINK ${ARCHDIR}/structqr.o ${OBJS} /OUT:${ARCHDIR}/structqr.exe
 ${ARCHDIR}/structqr: ${ARCHDIR}/structqr.o ${OBJS}
-	${CXX} ${CXXFLAGS} ${ARCHDIR}/structqr.o ${OBJS} -o ${ARCHDIR}/structqr -lm
+	${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/structqr.o ${OBJS} -o ${ARCHDIR}/structqr -lm
 ${ARCHDIR}/structqr.o: ${UTILSRCDIR}/structqr.cpp
 	${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/structqr.cpp $(COPTO)${ARCHDIR}/structqr.o
     
diff --git a/plugins/membrane/Makefile b/plugins/membrane/Makefile
index f92c426..38a9c06 100644
--- a/plugins/membrane/Makefile
+++ b/plugins/membrane/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = membrane.tcl pkgIndex.tcl \
 	popc_box.pdb popc_box.psf \
diff --git a/plugins/mergestructs/Makefile b/plugins/mergestructs/Makefile
index d6a4225..66ba9b2 100644
--- a/plugins/mergestructs/Makefile
+++ b/plugins/mergestructs/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = mergestructs.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/molefacture/Makefile b/plugins/molefacture/Makefile
index 96e70dc..8d10ef4 100644
--- a/plugins/molefacture/Makefile
+++ b/plugins/molefacture/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = molefacture.tcl molefacture_builder.tcl \
 	molefacture_edit.tcl molefacture_geometry.tcl molefacture_gui.tcl \
diff --git a/plugins/molfile_plugin/Makefile b/plugins/molfile_plugin/Makefile
index 18fb6dc..e32b130 100644
--- a/plugins/molfile_plugin/Makefile
+++ b/plugins/molfile_plugin/Makefile
@@ -1,7 +1,6 @@
 # Makefile for molecule file readers
 # $Id: vmd-1.8.7-gentoo.patch,v 1.2 2010/07/27 18:47:33 jlec Exp $
 
-.SILENT:
 
 .SUFFIXES:
 
@@ -14,8 +13,8 @@ INCDIR = -I../include -I${SRCDIR}
 
 VPATH = src ../include ${ARCHDIR}
 
-SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
-SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
+SCCFLAGS = $(CFLAGS) $(DEF)"STATIC_PLUGIN"
+SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN"
 
 #
 # Rules
diff --git a/plugins/molfile_plugin/src/cifplugin/Makefile b/plugins/molfile_plugin/src/cifplugin/Makefile
index 1dfa768..e3f380b 100644
--- a/plugins/molfile_plugin/src/cifplugin/Makefile
+++ b/plugins/molfile_plugin/src/cifplugin/Makefile
@@ -1,6 +1,5 @@
 # Makefile for molecule file readers
 
-.SILENT:
 
 .SUFFIXES:
 
@@ -14,7 +13,7 @@ INCDIR = -I../include -I${SRCDIR}
 VPATH = src ../include ${ARCHDIR}
 
 SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
-SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
+SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN"
 
 #
 # Rules
diff --git a/plugins/moltoptools/Makefile b/plugins/moltoptools/Makefile
index 3599cb7..8d80ec2 100644
--- a/plugins/moltoptools/Makefile
+++ b/plugins/moltoptools/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = moltoptools.tcl pkgIndex.tcl
 VMVERSION = 0.1
diff --git a/plugins/multimolanim/Makefile b/plugins/multimolanim/Makefile
index 09b4cb1..39b3139 100755
--- a/plugins/multimolanim/Makefile
+++ b/plugins/multimolanim/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = multimolanim.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/multiplot/Makefile b/plugins/multiplot/Makefile
index 520bf3e..a5b7bc5 100644
--- a/plugins/multiplot/Makefile
+++ b/plugins/multiplot/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = multiplot.tcl pkgIndex.tcl
 VMVERSION = 1.4
diff --git a/plugins/multitext/Makefile b/plugins/multitext/Makefile
index cc98bde..453c0da 100644
--- a/plugins/multitext/Makefile
+++ b/plugins/multitext/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = multitext.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/namdenergy/Makefile b/plugins/namdenergy/Makefile
index 9d4c11c..229f6cc 100644
--- a/plugins/namdenergy/Makefile
+++ b/plugins/namdenergy/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = namdenergy.tcl pkgIndex.tcl
 VMVERSION = 1.2
diff --git a/plugins/namdgui/Makefile b/plugins/namdgui/Makefile
index 2e25b19..c03d87b 100644
--- a/plugins/namdgui/Makefile
+++ b/plugins/namdgui/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = namdgui.tcl namdgui_tclforces.tcl pkgIndex.tcl
 VMVERSION = 1.2
diff --git a/plugins/namdplot/Makefile b/plugins/namdplot/Makefile
index e155387..88969e6 100644
--- a/plugins/namdplot/Makefile
+++ b/plugins/namdplot/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = namdplot.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/namdserver/Makefile b/plugins/namdserver/Makefile
index 378d203..84dcb24 100644
--- a/plugins/namdserver/Makefile
+++ b/plugins/namdserver/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = namdserver.tcl pkgIndex.tcl
 VMVERSION = 1.1
diff --git a/plugins/nanotube/Makefile b/plugins/nanotube/Makefile
index 6662cd5..deaf55c 100644
--- a/plugins/nanotube/Makefile
+++ b/plugins/nanotube/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = nanotube.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/navfly/Makefile b/plugins/navfly/Makefile
index 82d913b..0194be8 100644
--- a/plugins/navfly/Makefile
+++ b/plugins/navfly/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = navfly.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/navigate/Makefile b/plugins/navigate/Makefile
index 6d48c3e..cf18738 100644
--- a/plugins/navigate/Makefile
+++ b/plugins/navigate/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 COPYFILES = navigate.tcl pkgIndex.tcl
 DIR = $(PLUGINDIR)/noarch/tcl/navigate1.0
diff --git a/plugins/nlenergy/Makefile b/plugins/nlenergy/Makefile
index 8c028ca..3c295fd 100644
--- a/plugins/nlenergy/Makefile
+++ b/plugins/nlenergy/Makefile
@@ -1,6 +1,5 @@
 # Makefile for nlenergy
 
-.SILENT:
 
 .SUFFIXES: 
 
diff --git a/plugins/optimization/Makefile b/plugins/optimization/Makefile
index e38a9dc..4188e7f 100644
--- a/plugins/optimization/Makefile
+++ b/plugins/optimization/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = optimization.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/palettetool/Makefile b/plugins/palettetool/Makefile
index 6317657..166d423 100644
--- a/plugins/palettetool/Makefile
+++ b/plugins/palettetool/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = palettetool.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/paratool/Makefile b/plugins/paratool/Makefile
index 8f24cc1..cbf1618 100644
--- a/plugins/paratool/Makefile
+++ b/plugins/paratool/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = paratool.tcl paratool_atomedit.tcl paratool_aux.tcl \
           paratool_respcharges.tcl paratool_charmmcharges.tcl \
diff --git a/plugins/pbctools/Makefile b/plugins/pbctools/Makefile
index 164c456..bcf6851 100755
--- a/plugins/pbctools/Makefile
+++ b/plugins/pbctools/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = pbcbox.tcl pbcgui.tcl pbcjoin.tcl pbcset.tcl pbctools.tcl \
 	pbcunwrap.tcl pbcwrap.tcl pkgIndex.tcl
diff --git a/plugins/pdbtool/Makefile b/plugins/pdbtool/Makefile
index c05579d..3f120c5 100644
--- a/plugins/pdbtool/Makefile
+++ b/plugins/pdbtool/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = pdbtool.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/pmepot/Makefile b/plugins/pmepot/Makefile
index 1858d13..fa6ac36 100644
--- a/plugins/pmepot/Makefile
+++ b/plugins/pmepot/Makefile
@@ -1,6 +1,5 @@
 # Makefile for PME potential library
 
-.SILENT:
 
 .SUFFIXES: 
 
diff --git a/plugins/psfgen/Makefile b/plugins/psfgen/Makefile
index d9c7c85..0d9b80e 100644
--- a/plugins/psfgen/Makefile
+++ b/plugins/psfgen/Makefile
@@ -1,6 +1,5 @@
 # Makefile for psfgen
 
-.SILENT:
 
 .SUFFIXES: 
 
diff --git a/plugins/psfgen/Makefile.pluginio b/plugins/psfgen/Makefile.pluginio
index 29444f2..28a6213 100644
--- a/plugins/psfgen/Makefile.pluginio
+++ b/plugins/psfgen/Makefile.pluginio
@@ -5,7 +5,6 @@
 #     them itself, but at the moment this is a good short-term development
 #     path until we write something better.
 
-.SILENT:
 
 .SUFFIXES: 
 
diff --git a/plugins/qmtool/Makefile b/plugins/qmtool/Makefile
index a8aafff..2a45307 100644
--- a/plugins/qmtool/Makefile
+++ b/plugins/qmtool/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = qmtool.tcl qmtool_analysis.tcl qmtool_atomedit.tcl \
           qmtool_aux.tcl qmtool_charges.tcl qmtool_intcoor.tcl \
diff --git a/plugins/ramaplot/Makefile b/plugins/ramaplot/Makefile
index 29a1f23..be6e86a 100644
--- a/plugins/ramaplot/Makefile
+++ b/plugins/ramaplot/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 FILES = ramaplot.tcl pkgIndex.tcl
 VERSION = 1.1
diff --git a/plugins/readcharmmpar/Makefile b/plugins/readcharmmpar/Makefile
index fffb98e..d257edd 100644
--- a/plugins/readcharmmpar/Makefile
+++ b/plugins/readcharmmpar/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = readcharmmpar.tcl par_all27_prot_lipid_na.inp pkgIndex.tcl par_amber2charmm.inp
 VMVERSION = 1.1
diff --git a/plugins/readcharmmtop/Makefile b/plugins/readcharmmtop/Makefile
index 88c7ab5..c8cb771 100644
--- a/plugins/readcharmmtop/Makefile
+++ b/plugins/readcharmmtop/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = readcharmmtop.tcl pkgIndex.tcl top_all27_prot_lipid_na.inp top_all27_hybrid.inp top_amber2charmm.inp
 VMVERSION = 1.0
diff --git a/plugins/resptool/Makefile b/plugins/resptool/Makefile
index 1f20b70..80e01eb 100644
--- a/plugins/resptool/Makefile
+++ b/plugins/resptool/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = resptool.tcl pkgIndex.tcl
 VMVERSION = 1.1
diff --git a/plugins/rmsd/Makefile b/plugins/rmsd/Makefile
index 23df59b..c328322 100644
--- a/plugins/rmsd/Makefile
+++ b/plugins/rmsd/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = rmsd.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/rmsdtt/Makefile b/plugins/rmsdtt/Makefile
index c914531..62b14fd 100644
--- a/plugins/rmsdtt/Makefile
+++ b/plugins/rmsdtt/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = rmsdtt.tcl pkgIndex.tcl
 VMVERSION = 2.0
diff --git a/plugins/rnaview/Makefile b/plugins/rnaview/Makefile
index f020ca0..9ab6914 100644
--- a/plugins/rnaview/Makefile
+++ b/plugins/rnaview/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = rnaview.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/ruler/Makefile b/plugins/ruler/Makefile
index 146cc4c..a7864d1 100644
--- a/plugins/ruler/Makefile
+++ b/plugins/ruler/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = ruler.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/runante/Makefile b/plugins/runante/Makefile
index 0410d50..a8fbe81 100644
--- a/plugins/runante/Makefile
+++ b/plugins/runante/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = runante.tcl pkgIndex.tcl
 VMVERSION = 0.1
diff --git a/plugins/saltbr/Makefile b/plugins/saltbr/Makefile
index 7e4234a..f5358e2 100644
--- a/plugins/saltbr/Makefile
+++ b/plugins/saltbr/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = saltbr.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/solvate/Makefile b/plugins/solvate/Makefile
index b1c5d92..7dfcd9b 100644
--- a/plugins/solvate/Makefile
+++ b/plugins/solvate/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 SOLVFILES = wat.top wat.pdb wat.psf solvate.tcl pkgIndex.tcl
 SOLVVERSION = 1.3
diff --git a/plugins/ssrestraints/Makefile b/plugins/ssrestraints/Makefile
index 81b79d8..dca38e7 100644
--- a/plugins/ssrestraints/Makefile
+++ b/plugins/ssrestraints/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = ssrestraints.tcl ssrestraints_stride.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/stamp/Makefile b/plugins/stamp/Makefile
index f0fb515..c077d53 100644
--- a/plugins/stamp/Makefile
+++ b/plugins/stamp/Makefile
@@ -1,6 +1,5 @@
 # Makefile for stamp
 
-.SILENT:
 
 .SUFFIXES: 
 
@@ -101,7 +100,7 @@ OBJS = ${ARCHDIR}/a3to1.o \
 ${ARCHDIR}/stamp.exe: ${OBJS}
 	LINK ${OBJS} /OUT:${ARCHDIR}/stamp.exe
 ${ARCHDIR}/stamp: ${OBJS}
-	${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/stamp -lm
+	${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/stamp -lm
     
     
 # Objects.
diff --git a/plugins/stingtool/Makefile b/plugins/stingtool/Makefile
index d7b84fe..477a97c 100644
--- a/plugins/stingtool/Makefile
+++ b/plugins/stingtool/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = stingtool.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/symmetrytool/Makefile b/plugins/symmetrytool/Makefile
index 43adc25..6898a43 100644
--- a/plugins/symmetrytool/Makefile
+++ b/plugins/symmetrytool/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = symmetry.tcl pkgIndex.tcl
 VMVERSION = 1.2
diff --git a/plugins/textview/Makefile b/plugins/textview/Makefile
index 5e35a4a..ba98391 100644
--- a/plugins/textview/Makefile
+++ b/plugins/textview/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = textview.tcl pkgIndex.tcl
 VMVERSION = 1.1
diff --git a/plugins/timeline/Makefile b/plugins/timeline/Makefile
index 3b9e7ac..a09c572 100644
--- a/plugins/timeline/Makefile
+++ b/plugins/timeline/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = timeline.tcl pkgIndex.tcl
 VMVERSION = 2.0
diff --git a/plugins/topotools/Makefile b/plugins/topotools/Makefile
index a8af827..beb4b54 100644
--- a/plugins/topotools/Makefile
+++ b/plugins/topotools/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = pkgIndex.tcl README topotools.tcl topoatoms.tcl \
 	topobonds.tcl topoangles.tcl topodihedrals.tcl topoimpropers.tcl \
diff --git a/plugins/trunctraj/Makefile b/plugins/trunctraj/Makefile
index 624b3e6..991b4e1 100644
--- a/plugins/trunctraj/Makefile
+++ b/plugins/trunctraj/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = trunctraj.tcl pkgIndex.tcl
 VMVERSION = 1.5
diff --git a/plugins/updater/Makefile b/plugins/updater/Makefile
index 4e29538..3122421 100644
--- a/plugins/updater/Makefile
+++ b/plugins/updater/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = updater.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/utilities/Makefile b/plugins/utilities/Makefile
index df1ccf4..c18c048 100644
--- a/plugins/utilities/Makefile
+++ b/plugins/utilities/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = utilities.tcl pkgIndex.tcl
 VMVERSION = 1.0
diff --git a/plugins/vdna/Makefile b/plugins/vdna/Makefile
index f994198..dd2d57b 100644
--- a/plugins/vdna/Makefile
+++ b/plugins/vdna/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = vdna.tcl pkgIndex.tcl
 VMVERSION = 2.0
diff --git a/plugins/viewmaster/Makefile b/plugins/viewmaster/Makefile
index c5d1625..8d25c7e 100644
--- a/plugins/viewmaster/Makefile
+++ b/plugins/viewmaster/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = viewmaster.tcl pkgIndex.tcl
 VMVERSION = 2.2
diff --git a/plugins/vmdmovie/Makefile b/plugins/vmdmovie/Makefile
index 10af8e2..cacc294 100644
--- a/plugins/vmdmovie/Makefile
+++ b/plugins/vmdmovie/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = vmdmovie.tcl pkgIndex.tcl
 VMVERSION = 1.7
diff --git a/plugins/vmdtkcon/Makefile b/plugins/vmdtkcon/Makefile
index 5f6a05d..04de94f 100644
--- a/plugins/vmdtkcon/Makefile
+++ b/plugins/vmdtkcon/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 TKCONFILES = vmdtkcon.tcl tkcon-modified.tcl pkgIndex.tcl tkcon-2.3 README
 DIR = $(PLUGINDIR)/noarch/tcl/vmdtkcon1.1
diff --git a/plugins/volmapgui/Makefile b/plugins/volmapgui/Makefile
index 9ece112..57ec111 100644
--- a/plugins/volmapgui/Makefile
+++ b/plugins/volmapgui/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 COPYFILES = volmapgui.tcl pkgIndex.tcl
 DIR = $(PLUGINDIR)/noarch/tcl/volmapgui1.1
diff --git a/plugins/zoomseq/Makefile b/plugins/zoomseq/Makefile
index aa95b41..66ee516 100644
--- a/plugins/zoomseq/Makefile
+++ b/plugins/zoomseq/Makefile
@@ -1,4 +1,3 @@
-.SILENT:
 
 VMFILES = zoomseq.tcl pkgIndex.tcl
 VMVERSION = 1.1
diff --git a/vmd-1.8.7/configure b/vmd-1.8.7/configure
index f01944a..b04bade 100755
--- a/vmd-1.8.7/configure
+++ b/vmd-1.8.7/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="gentoo-bindir";
 
 # Directory where VMD files and executables are installed
-$install_library_dir="/usr/local/lib/$install_name";
+$install_library_dir="gentoo-libdir/$install_name";
 
 
 # optionally override hard-coded defaults above with environment variables
@@ -128,29 +128,6 @@ if ($ENV{VMDINSTALLLIBRARYDIR}) {
 # Configure script code begins here
 ############################################################################
 
-## Test for existence of a properly compiled plugin tree
-if (!(-e "plugins")) {
-  print "\n";
-  print "VMD plugin directory not found.\n";
-  print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
-  print "into a 'plugins' directory linked or located in this directory.\n";
-  print "Be sure your PLUGINDIR environment variable is set before running\n";
-  print "'make distrib' in the plugin build area.\n";
-  print "\n";
-  die "Halting configuration until VMD plugins are built.\n";
-} else {
-  if (!(-e "plugins/include/vmdplugin.h")) {
-    print "\n";
-    print "VMD plugin include files or directory not found.\n";
-    print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
-    print "into a 'plugins' directory linked or located in this directory.\n";
-    print "Be sure your PLUGINDIR environment variable is set before running\n";
-    print "'make distrib' in the plugin build area.\n";
-    print "\n";
-    die "Halting configuration until VMD plugins are built.\n";
-  }
-} 
-
 #################### Parse command line options   ###########
 # list of allowed architectures
 @archlist=('IRIX6', 'IRIX6_64', 'FREEBSD', 'HPUX11', 'AIX4', 'AIX5', 'AIX5_64', 'AIX6_64', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXIA64', 'LINUXPPC', 'LINUXPPC64', 'MACOSX', 'MACOSXX86', 'MACOSXX86_64', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');
@@ -435,7 +412,7 @@ chop($arch_no_math_float);
 
 ################ Plugin options
 #
-$plugin_dir	= "../plugins";
+$plugin_dir	= "gentoo-plugindir";
 $plugin_include = "-I$plugin_dir/include";
 $plugin_library = "";
 $plugin_libs    = "";
@@ -448,7 +425,7 @@ $plugin_defines = "";
 @plugin_extra   = ();
 
 if ($config_staticplugin) {
-  $molfile_dir = "$plugin_dir/$config_arch/molfile";
+  $molfile_dir = "$plugin_dir/compile/lib_LINUX/molfile";
   $plugin_include .= " -I$molfile_dir";
   $plugin_library .= " -L$molfile_dir";
   $plugin_libs    .= " -lmolfile_plugin";
@@ -550,8 +527,8 @@ $fltkopengl_defines     = "-DVMDOPENGL -DVMDFLTKOPENGL -DVMDGRAPHICS";
 ################ FLTK GUI
 $fltk_defines     = "-DVMDGUI -DVMDFLTK";
 $fltk_dir         = "$vmd_library_dir/fltk";
-$fltk_include     = "-I$fltk_dir/include";
-$fltk_library     = "-L$fltk_dir/$config_arch";
+$fltk_include     = "-Igentoo-fltk-include";
+$fltk_library     = "-Lgentoo-fltk-libs";
 $fltk_libs        = "-lfltk -lX11";
 #@fltk_cc          = ('forms_ui.c');
 @fltk_cu          = ();
@@ -612,8 +589,8 @@ $tcl_include      = "-I$stock_tcl_include_dir";
 if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; }
 $tcl_library      = "-L$stock_tcl_library_dir";
 if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; }
-$tcl_libs         = "-ltcl8.5";  
-if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; }
+$tcl_libs         = "-ltcl";  
+if ($config_tk) { $tcl_libs = "-ltk -lX11 " . $tcl_libs; }
 
 @tcl_cc           = ();
 @tcl_cu           = ();
@@ -938,8 +915,8 @@ $cuda_libs        = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart";
 #######################
 $netcdf_defines     = "";
 $netcdf_dir         = "$vmd_library_dir/netcdf";
-$netcdf_include     = "-I$netcdf_dir/include";
-$netcdf_library     = "-L$netcdf_dir/lib_$config_arch";
+$netcdf_include     = "-Igentoo-netcdf-include";
+$netcdf_library     = "-Lgentoo-netcdf-libs";
 $netcdf_libs        = "-lnetcdf";
 @netcdf_cc          = ();
 @netcdf_cu          = ();
@@ -1007,9 +984,9 @@ $pthreads_libs     = "-lpthread";
 $python_defines     = "-DVMDPYTHON";
 $python_dir         = "$vmd_library_dir/python";
 $numpy_dir          = "$vmd_library_dir/numpy";
-$python_include     = "-I$python_dir/lib_$config_arch/include/python2.5 -I$numpy_dir/lib_$config_arch/include -I$python_dir/lib_$config_arch/lib/python2.5/site-packages/numpy/core/include";
-$python_library     = "-L$python_dir/lib_$config_arch/lib/python2.5/config";
-$python_libs        = "-lpython2.5 -lpthread";
+$python_include     = "-Igentoo-python-include -Igentoo-numpy-include";
+$python_library     = "-Lgentoo-python-lib";
+$python_libs        = "-lgentoo-python-link -lpthread";
 @python_h           = ('PythonTextInterp.h',
                        'VMDTkinterMenu.h',
 		       'py_commands.h',
@@ -1621,8 +1598,8 @@ if ($config_arch eq "LINUX") {
 
     # XFree 4.0 Direct Rendering Interface and GLX 
     $opengl_dir         = "/usr/X11R6";
-    $opengl_include     = "-I$opengl_dir/include";
-    $opengl_library     = "-L$opengl_dir/lib";
+    $opengl_include     = "-Igentoo-opengl-include";
+    $opengl_library     = "-Lgentoo-opengl-libs";
     $opengl_libs        = "-lGL -lGLU"; 
     # $opengl_libs      = "-L/usr/X11R6/lib -lGL -lGLU -lXext -lX11";
 
@@ -1650,15 +1627,15 @@ if ($config_arch eq "LINUX") {
       $arch_lopts       .= "-i-static ";
     } else {
       # compling with GCC
-      $arch_cc          = "gcc";
-      $arch_ccpp        = "g++";
+      $arch_cc          = "gentoo-gcc";
+      $arch_ccpp        = "gentoo-g++";
       $arch_depend_flag = "-MM";
-      $arch_shld        = "g++ -shared";
+      $arch_shld        = "gentoo-g++ -shared";
       $arch_shlibname   = "so";
       $arch_shcppopts   = "-fPIC";
-      $arch_shldopts    = "";
-      $arch_opt_flag    = "-m32 -fno-for-scope -Wno-deprecated -Wall -O3";
-      $arch_copts       = "-m32 -Wall -O3";
+      $arch_shldopts    = "gentoo-ldflags";
+      $arch_opt_flag    = "gentoo-cflags";
+      $arch_copts       = "gentoo-cflags";
 
       if ($config_static) {
         $arch_lopts       = "-static";
@@ -1768,7 +1745,7 @@ if ($config_arch eq "LINUXAMD64") {
       $arch_template_repository = "foobar";
       $arch_shlibname   = "so";
       $arch_shcppopts   = "-fPIC";
-      $arch_shldopts    = "";
+      $arch_shldopts    = "gentoo-ldflags";
 
       if ($config_static) {
         # link everything statically (this won't work due to libGL issues)
@@ -2714,11 +2691,11 @@ LIBDIRS     = $LIBDIRS
 DEFINES     = $DEFINES
 
 # compiler and compiler directives 
-CC          = $arch_cc
-CFLAGS      = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
+CC          = gentoo-gcc
+CFLAGS      = gentoo-cflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
 
-CCPP	    = $arch_ccpp
-CPPFLAGS    = $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
+CCPP	    = gentoo-g++
+CPPFLAGS    = gentoo-cxxflags $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
 
 NVCC        = $arch_nvcc
 NVCCFLAGS   = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
@@ -2766,7 +2743,7 @@ $config_progname: y.tab.h \$(VMD_OBJS)
 	if [ ! -r ./$arch_template_repository ]; then \\
 	  ln -s $vmd_src_dir/$arch_template_repository ./$arch_template_repository ; \\
 	fi; \\
-	\$(CCPP) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; 
+	\$(CCPP) \$(LDFLAGS) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; 
 	\$(COMPILERC) \$(RCFLAGS)
 
 install:
@@ -2804,8 +2781,7 @@ install:
 	-\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir"
 	\$(CD) $vmd_bin_dir ; \\
 	if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\
-	if [ ! -x "/bin/csh" ]; then \\
-		\$(ECHO) "Info: /bin/csh shell not found, installing Bourne shell startup script instead" ; \\
+	if [ -x "/bin/bash" ]; then \\
 		\$(ECHO) '#!/bin/sh' >> run_vmd_tmp ; \\
 		\$(ECHO) 'defaultvmddir="$install_library_dir"' >> run_vmd_tmp ; \\
 		\$(ECHO) 'vmdbasename=vmd' >> run_vmd_tmp ; \\
diff --git a/vmd-1.8.7/src/Makefile b/vmd-1.8.7/src/Makefile
index 971a8c1..fe4c635 100755
--- a/vmd-1.8.7/src/Makefile
+++ b/vmd-1.8.7/src/Makefile
@@ -432,7 +432,7 @@ vmd_WIN32: y.tab.h $(VMD_OBJS)
 	if [ ! -r ./ ]; then \
 	  ln -s ../src/ ./ ; \
 	fi; \
-	$(CCPP) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; 
+	$(CCPP) $(LDFLAGS) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; 
 	$(COMPILERC) $(RCFLAGS)
 
 install: