Fix for new python ABIs, #316187; building netcdf plugin, #306893, thanks Kamil Kisiel for the patch; LDFLAGS are respected now; EAPI=3 and basic fixes for prefix, usability has to be tested

(Portage version: 2.2_rc67/cvs/Linux x86_64)

4 files changed, 2347 insertions, 14 deletions

diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
index b3eb6550c216..ad9cdc020285 100644
--- a/sci-chemistry/vmd/ChangeLog
+++ b/sci-chemistry/vmd/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/vmd
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.27 2010/02/23 18:00:14 alexxy Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.28 2010/05/18 07:22:51 jlec Exp $
+
+*vmd-1.8.7-r1 (18 May 2010)
+
+  18 May 2010; Justin Lecher <jlec@gentoo.org> +vmd-1.8.7-r1.ebuild,
+  files/vmd-1.8.7-config.patch, +files/vmd-1.8.7-gentoo.patch:
+  Fix for new python ABIs, #316187; building netcdf plugin, #306893, thanks
+  Kamil Kisiel for the patch; LDFLAGS are respected now; EAPI=3 and basic
+  fixes for prefix, usability has to be tested
 
   23 Feb 2010; Alexey Shvetsov <alexxy@gentoo.org> vmd-1.8.6-r1.ebuild,
   vmd-1.8.7.ebuild, metadata.xml:
diff --git a/sci-chemistry/vmd/files/vmd-1.8.7-config.patch b/sci-chemistry/vmd/files/vmd-1.8.7-config.patch
index 7850e9f32b6b..57d1bd9f6376 100644
--- a/sci-chemistry/vmd/files/vmd-1.8.7-config.patch
+++ b/sci-chemistry/vmd/files/vmd-1.8.7-config.patch
@@ -1,6 +1,923 @@
-diff -Naur vmd-1.8.7/configure vmd-1.8.7.new/configure
---- vmd-1.8.7/configure	2009-08-01 03:19:34.000000000 -0400
-+++ vmd-1.8.7.new/configure	2009-08-07 09:12:43.000000000 -0400
+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-config.patch,v 1.3 2010/05/18 07:22:51 jlec Exp $
+   
+-- .SILENT:
+   
+   .SUFFIXES:
+   
+@@ -17,7 +16,6 @@
+   # Makefile for molecule file readers
+   # $Id: vmd-1.8.7-config.patch,v 1.3 2010/05/18 07:22:51 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..ce75e33 100644
+--- a/plugins/catdcd/Makefile
++++ b/plugins/catdcd/Makefile
+@@ -1,6 +1,5 @@
+ # Makefile for catdcd
+ 
+-.SILENT:
+ 
+ .SUFFIXES: 
+ 
+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..f24fe29 100644
+--- a/plugins/cionize/Makefile
++++ b/plugins/cionize/Makefile
+@@ -1,6 +1,5 @@
+ # Makefile for cionize
+ 
+-#.SILENT:
+ 
+ .SUFFIXES: 
+ 
+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..265bb85 100644
+--- a/plugins/clustalw/Makefile
++++ b/plugins/clustalw/Makefile
+@@ -1,6 +1,5 @@
+ # Makefile for clustalw
+ 
+-.SILENT:
+ 
+ .SUFFIXES: 
+ 
+diff --git a/plugins/cluster/Makefile b/plugins/cluster/Makefile
+index 99d347e..a083e57 100644
+--- a/plugins/cluster/Makefile
++++ b/plugins/cluster/Makefile
+@@ -1,6 +1,5 @@
+ # Makefile for psfgen
+ 
+-.SILENT:
+ 
+ .SUFFIXES: 
+ 
+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..ba709a7 100644
+--- a/plugins/libbiokit/Makefile
++++ b/plugins/libbiokit/Makefile
+@@ -1,6 +1,5 @@
+ # Makefile for libbiokit
+ 
+-.SILENT:
+ 
+ .SUFFIXES: 
+ 
+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..f17bdda 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-config.patch,v 1.3 2010/05/18 07:22:51 jlec Exp $
+ 
+-.SILENT:
+ 
+ .SUFFIXES:
+ 
+diff --git a/plugins/molfile_plugin/src/cifplugin/Makefile b/plugins/molfile_plugin/src/cifplugin/Makefile
+index 1dfa768..88f4b7b 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:
+ 
+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..715be81 100644
+--- a/plugins/stamp/Makefile
++++ b/plugins/stamp/Makefile
+@@ -1,6 +1,5 @@
+ # Makefile for stamp
+ 
+-.SILENT:
+ 
+ .SUFFIXES: 
+ 
+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..051e04a 100755
+--- a/vmd-1.8.7/configure
++++ b/vmd-1.8.7/configure
 @@ -13,10 +13,10 @@
  $install_name = "vmd";
  
@@ -14,7 +931,7 @@ diff -Naur vmd-1.8.7/configure vmd-1.8.7.new/configure
  
  
  # optionally override hard-coded defaults above with environment variables
-@@ -128,29 +128,6 @@
+@@ -128,29 +128,6 @@ if ($ENV{VMDINSTALLLIBRARYDIR}) {
  # Configure script code begins here
  ############################################################################
  
@@ -44,7 +961,7 @@ diff -Naur vmd-1.8.7/configure vmd-1.8.7.new/configure
  #################### 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 @@
+@@ -435,7 +412,7 @@ chop($arch_no_math_float);
  
  ################ Plugin options
  #
@@ -53,7 +970,7 @@ diff -Naur vmd-1.8.7/configure vmd-1.8.7.new/configure
  $plugin_include = "-I$plugin_dir/include";
  $plugin_library = "";
  $plugin_libs    = "";
-@@ -448,7 +425,7 @@
+@@ -448,7 +425,7 @@ $plugin_defines = "";
  @plugin_extra   = ();
  
  if ($config_staticplugin) {
@@ -62,7 +979,7 @@ diff -Naur vmd-1.8.7/configure vmd-1.8.7.new/configure
    $plugin_include .= " -I$molfile_dir";
    $plugin_library .= " -L$molfile_dir";
    $plugin_libs    .= " -lmolfile_plugin";
-@@ -550,8 +527,8 @@
+@@ -550,8 +527,8 @@ $fltkopengl_defines     = "-DVMDOPENGL -DVMDFLTKOPENGL -DVMDGRAPHICS";
  ################ FLTK GUI
  $fltk_defines     = "-DVMDGUI -DVMDFLTK";
  $fltk_dir         = "$vmd_library_dir/fltk";
@@ -73,7 +990,7 @@ diff -Naur vmd-1.8.7/configure vmd-1.8.7.new/configure
  $fltk_libs        = "-lfltk -lX11";
  #@fltk_cc          = ('forms_ui.c');
  @fltk_cu          = ();
-@@ -612,8 +589,8 @@
+@@ -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"; }
@@ -84,7 +1001,7 @@ diff -Naur vmd-1.8.7/configure vmd-1.8.7.new/configure
  
  @tcl_cc           = ();
  @tcl_cu           = ();
-@@ -938,8 +915,8 @@
+@@ -938,8 +915,8 @@ $cuda_libs        = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart";
  #######################
  $netcdf_defines     = "";
  $netcdf_dir         = "$vmd_library_dir/netcdf";
@@ -95,7 +1012,7 @@ diff -Naur vmd-1.8.7/configure vmd-1.8.7.new/configure
  $netcdf_libs        = "-lnetcdf";
  @netcdf_cc          = ();
  @netcdf_cu          = ();
-@@ -1007,9 +984,9 @@
+@@ -1007,9 +984,9 @@ $pthreads_libs     = "-lpthread";
  $python_defines     = "-DVMDPYTHON";
  $python_dir         = "$vmd_library_dir/python";
  $numpy_dir          = "$vmd_library_dir/numpy";
@@ -108,7 +1025,7 @@ diff -Naur vmd-1.8.7/configure vmd-1.8.7.new/configure
  @python_h           = ('PythonTextInterp.h',
                         'VMDTkinterMenu.h',
  		       'py_commands.h',
-@@ -1621,8 +1598,8 @@
+@@ -1621,8 +1598,8 @@ if ($config_arch eq "LINUX") {
  
      # XFree 4.0 Direct Rendering Interface and GLX 
      $opengl_dir         = "/usr/X11R6";
@@ -119,7 +1036,7 @@ diff -Naur vmd-1.8.7/configure vmd-1.8.7.new/configure
      $opengl_libs        = "-lGL -lGLU"; 
      # $opengl_libs      = "-L/usr/X11R6/lib -lGL -lGLU -lXext -lX11";
  
-@@ -1650,15 +1627,15 @@
+@@ -1650,15 +1627,15 @@ if ($config_arch eq "LINUX") {
        $arch_lopts       .= "-i-static ";
      } else {
        # compling with GCC
@@ -132,11 +1049,44 @@ diff -Naur vmd-1.8.7/configure vmd-1.8.7.new/configure
 +      $arch_shld        = "gentoo-g++ -shared";
        $arch_shlibname   = "so";
        $arch_shcppopts   = "-fPIC";
-       $arch_shldopts    = "";
+-      $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)
+@@ -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:
diff --git a/sci-chemistry/vmd/files/vmd-1.8.7-gentoo.patch b/sci-chemistry/vmd/files/vmd-1.8.7-gentoo.patch
new file mode 100644
index 000000000000..c80ed09be17b
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.8.7-gentoo.patch
@@ -0,0 +1,1204 @@
+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 1.1 2010/05/18 07:22:51 jlec Exp $
+   
+-- .SILENT:
+   
+   .SUFFIXES:
+   
+@@ -17,7 +16,6 @@
+   # Makefile for molecule file readers
+   # $Id: vmd-1.8.7-gentoo.patch,v 1.1 2010/05/18 07:22:51 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..f17bdda 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 1.1 2010/05/18 07:22:51 jlec Exp $
+ 
+-.SILENT:
+ 
+ .SUFFIXES:
+ 
+diff --git a/plugins/molfile_plugin/src/cifplugin/Makefile b/plugins/molfile_plugin/src/cifplugin/Makefile
+index 1dfa768..88f4b7b 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:
+ 
+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..2763347 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)
+@@ -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:
diff --git a/sci-chemistry/vmd/vmd-1.8.7-r1.ebuild b/sci-chemistry/vmd/vmd-1.8.7-r1.ebuild
new file mode 100644
index 000000000000..0d228694d500
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.8.7-r1.ebuild
@@ -0,0 +1,171 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.8.7-r1.ebuild,v 1.1 2010/05/18 07:22:51 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2"
+
+inherit eutils multilib python toolchain-funcs
+
+DESCRIPTION="Visual Molecular Dynamics"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+SRC_URI="${P}.src.tar.gz"
+
+SLOT="0"
+LICENSE="vmd"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE="tachyon"
+
+RESTRICT="fetch"
+
+# currently, tk-8.5* with USE=truetype breaks some
+# tk apps such as Sequence Viewer or Timeline.
+DEPEND="
+	|| (
+		>=dev-lang/tk-8.5[-truetype]
+		=dev-lang/tk-8.4*
+	)
+	dev-lang/perl
+	dev-python/numpy
+	sci-biology/stride
+	sci-libs/netcdf
+	virtual/opengl
+	x11-libs/fltk:1.1
+	x11-libs/libXft"
+
+RDEPEND="${DEPEND}
+	x11-terms/xterm
+	tachyon? ( media-gfx/tachyon )"
+
+VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
+# Binary only plugin!!
+QA_TEXTRELS="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
+QA_PRESTRIPPED="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
+QA_DT_HASH_amd64="usr/lib64/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
+QA_DT_HASH_x86="usr/lib/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
+
+pkg_nofetch() {
+	elog "Please download ${SRC_URI} from"
+	elog "${VMD_DOWNLOAD}"
+	elog "after agreeing to the license and then move it to "
+	elog "${DISTDIR}"
+}
+
+src_prepare() {
+	# apply LINUX-arch patches to vmd configure
+	cd "${WORKDIR}" && epatch "${FILESDIR}/${P}-gentoo.patch"
+
+	# prepare the plugins
+	cd "${WORKDIR}"/plugins
+
+	sed -e "s:CC = gcc:CC = $(tc-getCC):" \
+		-e "s:CXX = g++:CXX = $(tc-getCXX):" \
+		-e "s:COPTO =.*\":COPTO = -fPIC -o\":" \
+		-e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o\":" \
+		-e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \
+		-e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \
+		-e "s:SHLD = gcc:SHLD = $(tc-getCC):" \
+		-e "s:-ltcl8.5:-ltcl:" \
+		-i Make-arch || die "Failed to set up plugins Makefile"
+
+	# prepare vmd itself
+	cd "${S}"
+
+	sed -e "s:gentoo-bindir:${ED}/usr/bin:" \
+		-e "s:gentoo-libdir:${ED}/usr/$(get_libdir):" \
+		-i configure || die "failed to adjust install paths"
+
+	sed -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:" \
+		-e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):" \
+		-i configure || die "failed to adjust OpenGL paths"
+
+	sed -e "s:gentoo-gcc:$(tc-getCC):" \
+		-e "s:gentoo-g++:$(tc-getCXX):" \
+		-e "s:gentoo-cflags:${CFLAGS}:" \
+		-e "s:gentoo-ldflags:${LDFLAGS}:g" \
+		-i configure || die "Failed to adjust C compiler/flags"
+
+	sed -e "s:gentoo-plugindir:${WORKDIR}/plugins:" \
+		-i configure || die "Failed to set up linking to plugin files"
+
+	sed -e "s:gentoo-fltk-include:${EPREFIX}/usr/include/fltk-1.1:" \
+		-e "s:gentoo-fltk-libs:${EPREFIX}/usr/$(get_libdir)/fltk-1.1:" \
+		-i configure || die "failed setting up fltk"
+
+	sed -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:" \
+		-e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):" \
+		-i configure || die "failed to set up netcdf"
+
+	local NUMPY_INCLUDE="numpy/core/include"
+	sed -e "s:gentoo-python-include:$(python_get_includedir):" \
+		-e "s:gentoo-python-lib:$(python_get_libdir):" \
+		-e "s:gentoo-python-link:$(PYTHON):" \
+		-e "s:gentoo-numpy-include:$(python_get_sitedir)/${NUMPY_INCLUDE}:" \
+		-i configure || die "failed setting up python"
+
+	sed -e "s:LINUXPPC:LINUX:g" \
+		-e "s:LINUXALPHA:LINUX:g" \
+		-e "s:LINUXAMD64:LINUX:g" \
+		-i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script"
+}
+
+src_configure() {
+	local myconfig="LINUX OPENGL FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY"
+	rm -f configure.options && echo $myconfig >> configure.options
+
+	./configure &> /dev/null || die "failed to configure"
+}
+
+src_compile() {
+	# build plugins
+	cd "${WORKDIR}"/plugins
+
+	emake -j1 \
+		LINUX TCLINC="-I${EPREFIX}/usr/include" \
+		TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" \
+		NETCDFLIB="-L${EPREFIX}/usr/$(get_libdir)" \
+		NETCDFINC="-I${EPREFIX}/usr/include" \
+		NETCDFLDFLAGS="-lnetcdf" \
+		|| die "failed to build plugins"
+
+	# build vmd
+	cd "${S}"/src
+	emake || die "failed to build vmd"
+}
+
+src_install() {
+	# install plugins
+	cd "${WORKDIR}"/plugins
+	PLUGINDIR=${D}/usr/$(get_libdir)/${PN}/plugins make distrib || \
+		die "failed to install plugins"
+
+	# install vmd
+	cd "${S}"/src
+	make install || die "failed to install vmd"
+
+	# export STRIDE_BIN so VMD knows where to find stride
+	echo "STRIDE_BIN=${EPREFIX}/usr/bin/stride" > "${T}"/99${PN} || \
+		die "Failed to create vmd env file"
+	doenvd "${T}"/99${PN} || die "Failed to install vmd env file"
+
+	# install docs
+	cd "${S}"
+	dodoc Announcement README doc/ig.pdf doc/ug.pdf
+
+	# remove some of the things we don't want and need in
+	# /usr/lib
+	cd "${ED}"/usr/$(get_libdir)/vmd
+	rm -fr doc README Announcement LICENSE || \
+		die "failed to clean up /usr/lib/vmd directory"
+
+	# adjust path in vmd wrapper
+	sed -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \
+		|| die "failed to set up vmd wrapper script"
+
+	# install icon and generate desktop entry
+	insinto /usr/share/pixmaps
+	doins "${FILESDIR}"/vmd.png || die "Failed to install vmd icon"
+	insinto /usr/share/applications
+	doins "${FILESDIR}"/vmd.desktop || die "Failed to install desktop entry"
+}