namd, charm: moved to the main tree.

12 files changed, 0 insertions, 812 deletions

diff --git a/sci-chemistry/namd/ChangeLog b/sci-chemistry/namd/ChangeLog
deleted file mode 100644
index 58ba2ec..0000000
--- a/sci-chemistry/namd/ChangeLog
+++ /dev/null
@@ -1,48 +0,0 @@
-# ChangeLog for sci-chemistry/namd
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/ChangeLog,v 1.9 2009/09/23 19:55:56 patrick Exp $
-
-  23 Sep 2009; Patrick Lauer <patrick@gentoo.org> namd-2.6.ebuild,
-  namd-2.7.ebuild:
-  Remove virtual/libc
-
-*namd-2.7 (08 Jun 2009)
-
-  08 Jun 2009; Jeff Gardner <je_fro@gentoo.org> namd-2.6.ebuild,
-  +namd-2.7.ebuild, +files/namd-2.7-gentoo.patch:
-  Latest version for testing. If anyone wants to modify and test on x86
-  please feel free :)
-
-  03 Jun 2008; Michael Sterrett <mr_bones_@gentoo.org> namd-2.6.ebuild:
-  remove reference to app-shells/csh which has been removed
-
-  07 Jan 2007; Danny van Dyk <kugelfang@gentoo.org> -namd-2.6_beta1.ebuild:
-  QA: Removed unused versions.
-
-  20 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
-  (#148281) Change herd to sci-chemistry from sci.
-
-*namd-2.6 (19 Sep 2006)
-
-  19 Sep 2006; Markus Dittrich <markusle@gentoo.org>
-  +files/namd-2.6-gentoo.patch, +namd-2.6.ebuild:
-  Version bump. This fixes bug #148146.
-
-  22 Dec 2005; Markus Dittrich <markusle@gentoo.org> namd-2.6_beta1.ebuild:
-  removed from package.mask and marked ~x86. Added app-shells/tcsh as
-  alternative to app-shells/csh in DEPEND.
-
-  10 Nov 2005; Markus Dittrich <markusle@gentoo.org> metadata.xml,
-  namd-2.6_beta1.ebuild:
-  Changed charm dependency to sys-cluster/charm since charm
-  has moved from sci-libs/charm to sys-cluster/charm
-
-*namd-2.6_beta1 (05 Oct 2005)
-
-  05 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
-  +files/namd-barrier-fix-gentoo.patch, +files/namd-fftw-lib-gentoo.patch,
-  +files/namd-makefile-gentoo.patch, +files/namd-tcl-lib-gentoo.patch,
-  +metadata.xml, +namd-2.6_beta1.ebuild:
-  Initial import. Ebuild contributed by Markus Dittrich <markusle@gmail.com>
-  (bug #108033).
-
diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest
deleted file mode 100644
index c6efd5d..0000000
--- a/sci-chemistry/namd/Manifest
+++ /dev/null
@@ -1,13 +0,0 @@
-AUX namd-2.6-gentoo.patch 3650 RMD160 e7cc7fa0e20b01295d6f7c83211f961720e8beaa SHA1 f5525811cc092c5125be93cdce0e8c4e22fbee38 SHA256 55fad22d757d83d786b279a50a724499fb915767ade827895d686df16fa829d9
-AUX namd-2.7-gentoo.patch 4046 RMD160 a7d087c47088d9a8df8f804e023d1a882e281e74 SHA1 333fe98dcfb54736f192f3baa82280dcab1fbd21 SHA256 9416859fa9f065f3f269441cbbb44d4f627b71c8cba29ba9e6765c08dae3611f
-AUX namd-2.7_beta2-gentoo.patch 4409 RMD160 301bc17156f10a552eae4c2b3ed91ed2ea9fae6a SHA1 3cb0deb35e690156cf1a41e35482fab42480e3af SHA256 c56728dbf426540f9558db31f7e45cacc654112022f42917e715dbaa6c05373d
-AUX namd-barrier-fix-gentoo.patch 2362 RMD160 c6b045a0f2ec9f29bf7f98db7a71c1533f2a20d3 SHA1 5d42ef58f08914ecdf4afe735345ff1264389544 SHA256 f0186fada88b387c0681095174be336d61b2968197d223c15c840c1ca96e4992
-AUX namd-fftw-lib-gentoo.patch 528 RMD160 bb776e58497f0ec672bf5fc9ef22d0717d8c27ad SHA1 b8ca7a0521900bd9dbf725d9ce7ed809ff2d1aa0 SHA256 04528fd52f70cccbba1ccf844b97b256a35f9b1b85ca3ef8a56b4c9308b22696
-AUX namd-makefile-gentoo.patch 2804 RMD160 e52934e5a1aa7ed34e270dc11e780b1bdef3011d SHA1 22d5bd779a280c1287c936dd855f8359fa7b1b4e SHA256 f3945ae8fff113286847d61a00d5a749b1c3a00b65394085e56ff47a0a209250
-AUX namd-tcl-lib-gentoo.patch 576 RMD160 0992dd4103b97baed85e66a8d4fc04c3991bedd1 SHA1 f1cc944b14f7f77785f1a914d3d50f44d9929aec SHA256 7a57497410f5791b1b9fa0535e66137bd1b4c5008e0253c7467bc40af7b6ac01
-DIST NAMD_2.7b1_Source.tar.gz 26302404 RMD160 ccb73606d3f0724c55ce022aa130656444825f5e SHA1 955e096a6c70e1e7786d10334bec3cae1eb4fff6 SHA256 cf48b659667fe9e03af27c8d434567525e924ebd08c801321c71361a8f166b2e
-DIST NAMD_2.7b2_Source.tar.gz 9094631 RMD160 ec2c46f6cdb582dca73ebdbd894a9827f2e276d9 SHA1 0acab2a3bb6fca67b767f02bf7d2d2045ce6c3b9 SHA256 5675eb08534a6e4ea7a59e52e949991b3ba42abd78b45a46976ac3d7ed3b8d67
-EBUILD namd-2.7_beta1.ebuild 2650 RMD160 34bd38adf5e1633871579048f5cba8f145ccd437 SHA1 72c6bd74a6f2903207b065568fc9bcbcfed9b027 SHA256 4e076659e7cdcfea5e2723f60db23a8361c7bbf0fc4a224d9f815b9e45690b1f
-EBUILD namd-2.7_beta2.ebuild 2822 RMD160 868febd53f7d9fd706ea92b471d74b7d0e0e3794 SHA1 97f5f26a35acbb6da314eeef3097fff736f9a48b SHA256 f60ad9ecb1a0d6d3f87712b122c6960c4d98880d926dcdb3bbd4de5b492b1c1b
-MISC ChangeLog 1847 RMD160 75be9b2bd8410d67c529e71e39641bb6de3c38a5 SHA1 db8521aebafd677935171bfc4750f6c0ada24693 SHA256 588112965c57b399bb488e3d2285b0044374c06706262be7fdbcba1591acaa1c
-MISC metadata.xml 282 RMD160 539a53475b01291eadb86c8c53a0fbc02b4a34d4 SHA1 7f42dcea44641b8a77ab9644791344ec6ed6c327 SHA256 3c1785eb4ab63774ed3a6b1bddd602ef24cd6795f690bb3289d5a980bca06349
diff --git a/sci-chemistry/namd/files/namd-2.6-gentoo.patch b/sci-chemistry/namd/files/namd-2.6-gentoo.patch
deleted file mode 100644
index 9a71de8..0000000
--- a/sci-chemistry/namd/files/namd-2.6-gentoo.patch
+++ /dev/null
@@ -1,107 +0,0 @@
-diff -Naur NAMD_2.6_Source/Makefile NAMD_2.6_Source.new/Makefile
---- NAMD_2.6_Source/Makefile	2006-08-30 00:19:25.000000000 -0400
-+++ NAMD_2.6_Source.new/Makefile	2006-09-19 15:56:17.000000000 -0400
-@@ -232,10 +232,10 @@
- 	$(DSTDIR)/stringhash.o
- 
- # definitions for Charm routines
--CHARMC = $(CHARM)/bin/charmc
--CHARMXI = $(CHARM)/bin/charmc
--CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1
--CHARMLIB = $(CHARM)/lib
-+CHARMC = /usr/bin/charmc
-+CHARMXI = /usr/bin/charmc
-+CHARMINC = /usr/include/charm-5.9 $(COPTD)CMK_OPTIMIZE=1
-+CHARMLIB = /usr/lib
- 
- # Libraries we may have changed
- LIBS = $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL)
-@@ -255,7 +255,7 @@
- 
- # Add new executables here.
- 
--BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb
-+BINARIES = namd2 psfgen flipdcd flipbinpdb
- 
- # This should be rebuilt at every compile, but not on Win32.
- BUILDINFO = $(DSTDIR)/buildinfo
-@@ -284,11 +284,6 @@
- 	$(CHARMOPTS) \
- 	-lm -o namd2
- 
--charmrun: $(CHARM)/bin/charmrun # XXX
--	$(COPY) $(CHARM)/bin/charmrun $@
--
--windowsbinaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
--
- namd2.exe:  $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
- 	$(MAKEBUILDINFO)
- 	$(CHARMC) -verbose \
-@@ -309,9 +304,6 @@
- charmd_faceless.exe:
- 	$(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
- 
--charmrun.exe:
--	$(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
--
- psfgen:	$(DSTDIR) $(SBOBJS)
- 	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
- 
-@@ -571,9 +563,7 @@
- 
- DOC_FILES = README.txt announce.txt license.txt notes.txt
- 
--RELEASE_FILES = flipdcd flipbinpdb psfgen charmrun namd2
--
--WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmrun.exe charmd.exe charmd_faceless.exe $(TCLDLL)
-+RELEASE_FILES = flipdcd flipbinpdb psfgen namd2
- 
- release: all
- 	$(ECHO) Creating release $(RELEASE_DIR_NAME)
-@@ -582,17 +572,9 @@
- 	for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done
- 	cp -r .rootdir/lib $(RELEASE_DIR_NAME)
- 	/bin/rm -rf $(RELEASE_DIR_NAME)/lib/CVS $(RELEASE_DIR_NAME)/lib/*/CVS
--	if [ -r $(CHARM)/bin/charmd ]; then \
--	  $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \
--	fi
--	if [ -r $(CHARM)/bin/charmd_faceless ]; then \
--	  $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \
--	fi
- 	chmod -R a+rX $(RELEASE_DIR_NAME)
- 	tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME)
- 	gzip $(RELEASE_DIR_NAME).tar
--	echo $(CHARM)
--	ls -l $(CHARM)/lib
- 	-for f in $(RELEASE_FILES); do echo $$f; $(LDD) $$f; done
- 
- winrelease: winall
-diff -Naur NAMD_2.6_Source/arch/Linux-i686.fftw NAMD_2.6_Source.new/arch/Linux-i686.fftw
---- NAMD_2.6_Source/arch/Linux-i686.fftw	2004-02-20 17:38:36.000000000 -0500
-+++ NAMD_2.6_Source.new/arch/Linux-i686.fftw	2006-09-19 15:52:32.000000000 -0400
-@@ -1,7 +1,7 @@
- 
--FFTDIR=/Projects/namd2/fftw/linux
--FFTINCL=-I$(FFTDIR)/include -I$(HOME)/fftw/include
--FFTLIB=-L$(FFTDIR)/lib -L$(HOME)/fftw/lib -lsrfftw -lsfftw
-+#FFTDIR=/Projects/namd2/fftw/linux
-+FFTINCL=-I/usr/include 
-+FFTLIB=-L/usr/lib -lsrfftw -lsfftw
- FFTFLAGS=-DNAMD_FFTW
- FFT=$(FFTINCL) $(FFTFLAGS)
- 
-diff -Naur NAMD_2.6_Source/arch/Linux-i686.tcl NAMD_2.6_Source.new/arch/Linux-i686.tcl
---- NAMD_2.6_Source/arch/Linux-i686.tcl	2004-10-27 17:40:55.000000000 -0400
-+++ NAMD_2.6_Source.new/arch/Linux-i686.tcl	2006-09-19 15:56:45.000000000 -0400
-@@ -1,8 +1,8 @@
- 
--TCLDIR=/Projects/namd2/tcl/linux
-+#TCLDIR=/Projects/namd2/tcl/linux
- #TCLDIR=$(HOME)/tcl/cray-xt3
--TCLINCL=-I$(TCLDIR)/include -I$(HOME)/tcl/include
--TCLLIB=-L$(TCLDIR)/lib -L$(HOME)/tcl/lib -ltcl8.3 -ldl
-+TCLINCL=-I/usr/include 
-+TCLLIB=-L/usr/lib -L$(HOME)/tcl/lib -ltcl -ldl
- TCLFLAGS=-DNAMD_TCL -DUSE_NON_CONST
- TCL=$(TCLINCL) $(TCLFLAGS)
- 
diff --git a/sci-chemistry/namd/files/namd-2.7-gentoo.patch b/sci-chemistry/namd/files/namd-2.7-gentoo.patch
deleted file mode 100644
index 733ee8e..0000000
--- a/sci-chemistry/namd/files/namd-2.7-gentoo.patch
+++ /dev/null
@@ -1,117 +0,0 @@
-diff -aurN NAMD_2.7b1_Source.orig/Make.charm NAMD_2.7b1_Source/Make.charm
---- NAMD_2.7b1_Source.orig/Make.charm	2009-06-07 15:15:11.000000000 -0500
-+++ NAMD_2.7b1_Source/Make.charm	2009-06-07 15:15:11.000000000 -0500
-@@ -2,5 +2,5 @@
- # The config script will override this setting if there is a directory
- # called charm-6.1 or charm in the NAMD base directory.
- 
--CHARMBASE = /Projects/namd2/charm-6.1
-+CHARMBASE = /usr/include/charm-6.1.2
- 
-diff -aurN NAMD_2.7b1_Source.orig/Makefile NAMD_2.7b1_Source/Makefile
---- NAMD_2.7b1_Source.orig/Makefile	2009-06-07 15:15:11.000000000 -0500
-+++ NAMD_2.7b1_Source/Makefile	2009-06-07 15:15:11.000000000 -0500
-@@ -297,10 +297,10 @@
- 	$(DSTDIR)/stringhash.o
- 
- # definitions for Charm routines
--CHARMC = $(CHARM)/bin/charmc
--CHARMXI = $(CHARM)/bin/charmc
--CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1
--CHARMLIB = $(CHARM)/lib
-+CHARMC = /usr/bin/charmc
-+CHARMXI = /usr/bin/charmc
-+CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1
-+CHARMLIB = /usr/gentoo-libdir
- 
- # Libraries we may have changed
- LIBS = $(CUDAOBJS) $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL)
-@@ -320,7 +320,7 @@
- 
- # Add new executables here.
- 
--BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb
-+BINARIES = namd2 psfgen flipdcd flipbinpdb
- 
- # This should be rebuilt at every compile, but not on Win32.
- BUILDINFO = $(DSTDIR)/buildinfo
-@@ -351,14 +351,6 @@
- 	$(CHARMOPTS) \
- 	-lm -o namd2
- 
--charmrun: $(CHARM)/bin/charmrun # XXX
--	$(COPY) $(CHARM)/bin/charmrun $@
--
--WINDOWSBINARIES = namd2.exe psfgen.exe
--# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
--
--windowsbinaries: $(WINDOWSBINARIES)
--
- namd2.exe:  $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) $(TCLDLL)
- 	$(MAKEBUILDINFO)
- 	$(CHARMC) -verbose \
-@@ -381,9 +373,6 @@
- charmd_faceless.exe:
- 	$(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
- 
--charmrun.exe:
--	$(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
--
- psfgen:	$(DSTDIR) $(SBOBJS) $(PLUGINOBJS)
- 	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
- 
-@@ -700,9 +689,7 @@
- 
- DOC_FILES = README.txt announce.txt license.txt notes.txt
- 
--RELEASE_FILES = flipdcd flipbinpdb psfgen charmrun namd2
--
--WINDOWS_RELEASE_FILES = $(WINDOWSBINARIES) $(TCLDLL)
-+RELEASE_FILES = flipdcd flipbinpdb psfgen namd2
- 
- release: all
- 	$(ECHO) Creating release $(RELEASE_DIR_NAME)
-@@ -711,17 +698,9 @@
- 	for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done
- 	cp -r .rootdir/lib $(RELEASE_DIR_NAME)
- 	/bin/rm -rf $(RELEASE_DIR_NAME)/lib/CVS $(RELEASE_DIR_NAME)/lib/*/CVS
--	if [ -r $(CHARM)/bin/charmd ]; then \
--	  $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \
--	fi
--	if [ -r $(CHARM)/bin/charmd_faceless ]; then \
--	  $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \
--	fi
- 	chmod -R a+rX $(RELEASE_DIR_NAME)
- 	tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME)
- 	gzip $(RELEASE_DIR_NAME).tar
--	echo $(CHARM)
--	ls -l $(CHARM)/lib
- 	-for f in $(RELEASE_FILES); do echo $$f; $(LDD) $$f; done
- 
- winrelease: winall
-diff -aurN NAMD_2.7b1_Source.orig/arch/Linux-x86_64.fftw NAMD_2.7b1_Source/arch/Linux-x86_64.fftw
---- NAMD_2.7b1_Source.orig/arch/Linux-x86_64.fftw	2009-06-07 15:15:11.000000000 -0500
-+++ NAMD_2.7b1_Source/arch/Linux-x86_64.fftw	2009-06-07 15:15:11.000000000 -0500
-@@ -1,7 +1,7 @@
- 
--FFTDIR=/Projects/namd2/fftw/linux-x86_64
-+FFTDIR=/usr
- FFTINCL=-I$(FFTDIR)/include
--FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw
-+FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw
- FFTFLAGS=-DNAMD_FFTW
- FFT=$(FFTINCL) $(FFTFLAGS)
- 
-diff -aurN NAMD_2.7b1_Source.orig/arch/Linux-x86_64.tcl NAMD_2.7b1_Source/arch/Linux-x86_64.tcl
---- NAMD_2.7b1_Source.orig/arch/Linux-x86_64.tcl	2009-06-07 15:15:11.000000000 -0500
-+++ NAMD_2.7b1_Source/arch/Linux-x86_64.tcl	2009-06-07 18:25:07.000000000 -0500
-@@ -1,7 +1,7 @@
- 
--TCLDIR=/Projects/namd2/tcl/linux-x86_64
-+TCLDIR=/usr
- TCLINCL=-I$(TCLDIR)/include
--TCLLIB=-L$(TCLDIR)/lib -ltcl8.3 -ldl
-+TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl
- TCLFLAGS=-DNAMD_TCL
- TCL=$(TCLINCL) $(TCLFLAGS)
- 
diff --git a/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch b/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch
deleted file mode 100644
index 898d6b5..0000000
--- a/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch
+++ /dev/null
@@ -1,126 +0,0 @@
-diff -ur NAMD_2.7b2_Source.orig//arch/Linux-x86_64.fftw NAMD_2.7b2_Source//arch/Linux-x86_64.fftw
---- NAMD_2.7b2_Source.orig//arch/Linux-x86_64.fftw	2010-04-23 14:40:54.566510874 -0500
-+++ NAMD_2.7b2_Source//arch/Linux-x86_64.fftw	2010-04-23 14:41:08.106528893 -0500
-@@ -1,7 +1,7 @@
- 
--FFTDIR=/Projects/namd2/fftw/linux-x86_64
-+FFTDIR=/usr
- FFTINCL=-I$(FFTDIR)/include
--FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw
-+FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw
- FFTFLAGS=-DNAMD_FFTW
- FFT=$(FFTINCL) $(FFTFLAGS)
- 
-diff -ur NAMD_2.7b2_Source.orig//arch/Linux-x86_64.tcl NAMD_2.7b2_Source//arch/Linux-x86_64.tcl
---- NAMD_2.7b2_Source.orig//arch/Linux-x86_64.tcl	2010-04-23 14:40:54.566510874 -0500
-+++ NAMD_2.7b2_Source//arch/Linux-x86_64.tcl	2010-04-23 14:41:08.106528893 -0500
-@@ -1,7 +1,7 @@
- 
--TCLDIR=/Projects/namd2/tcl/linux-x86_64
-+TCLDIR=/usr
- TCLINCL=-I$(TCLDIR)/include
--TCLLIB=-L$(TCLDIR)/lib -ltcl8.3 -ldl
-+TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl
- TCLFLAGS=-DNAMD_TCL
- TCL=$(TCLINCL) $(TCLFLAGS)
- 
-diff -ur NAMD_2.7b2_Source.orig//Make.charm NAMD_2.7b2_Source//Make.charm
---- NAMD_2.7b2_Source.orig//Make.charm	2010-04-23 14:40:54.556517020 -0500
-+++ NAMD_2.7b2_Source//Make.charm	2010-04-23 14:42:16.026530011 -0500
-@@ -2,5 +2,5 @@
- # The config script will override this setting if there is a directory
- # called charm-6.1 or charm in the NAMD base directory.
- 
--CHARMBASE = /Projects/namd2/charm-6.1.3
-+CHARMBASE = /usr/include/charm-6.1.3
- 
-Only in NAMD_2.7b2_Source/: Make.charm.~1~
-Only in NAMD_2.7b2_Source/: Make.charm.porig
-diff -ur NAMD_2.7b2_Source.orig//Makefile NAMD_2.7b2_Source//Makefile
---- NAMD_2.7b2_Source.orig//Makefile	2010-04-23 14:40:54.556517020 -0500
-+++ NAMD_2.7b2_Source//Makefile	2010-04-23 14:42:59.446523306 -0500
-@@ -300,10 +300,10 @@
- 	$(DSTDIR)/stringhash.o
- 
- # definitions for Charm routines
--CHARMC = $(CHARM)/bin/charmc
--CHARMXI = $(CHARM)/bin/charmc
--CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1
--CHARMLIB = $(CHARM)/lib
-+CHARMC = /usr/bin/charmc
-+CHARMXI = /usr/bin/charmc
-+CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1
-+CHARMLIB = /usr/gentoo-libdir
- 
- # Libraries we may have changed
- LIBS = $(CUDAOBJS) $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL)
-@@ -323,7 +323,7 @@
- 
- # Add new executables here.
- 
--BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb
-+BINARIES = namd2 psfgen flipdcd flipbinpdb
- 
- # This should be rebuilt at every compile, but not on Win32.
- BUILDINFO = $(DSTDIR)/buildinfo
-@@ -354,9 +354,6 @@
- 	$(CHARMOPTS) \
- 	-lm -o namd2
- 
--charmrun: $(CHARM)/bin/charmrun # XXX
--	$(COPY) $(CHARM)/bin/charmrun $@
--
- $(LIBCUDARTSO):
- 	if [ -r $(CUDADIR)/lib64/$(LIBCUDARTSO) ]; then \
- 	  $(COPY) $(CUDADIR)/lib64/$(LIBCUDARTSO) $@; \
-@@ -364,10 +361,6 @@
- 	  $(COPY) $(CUDADIR)/lib/$(LIBCUDARTSO) $@; \
- 	fi
- 
--WINDOWSBINARIES = namd2.exe psfgen.exe
--# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
--windowsbinaries: $(WINDOWSBINARIES)
--
- namd2.exe:  $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) $(TCLDLL)
- 	$(MAKEBUILDINFO)
- 	$(CHARMC) -verbose \
-@@ -390,9 +383,6 @@
- charmd_faceless.exe:
- 	$(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
- 
--charmrun.exe:
--	$(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
--
- psfgen:	$(DSTDIR) $(SBOBJS) $(PLUGINOBJS)
- 	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
- 
-@@ -716,9 +706,7 @@
- 
- DOC_FILES = README.txt announce.txt license.txt notes.txt
- 
--RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen charmrun namd2
--
--WINDOWS_RELEASE_FILES = $(WINDOWSBINARIES) $(TCLDLL)
-+RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen namd2
- 
- release: all
- 	$(ECHO) Creating release $(RELEASE_DIR_NAME)
-@@ -727,17 +715,9 @@
- 	for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done
- 	cp -r .rootdir/lib $(RELEASE_DIR_NAME)
- 	/bin/rm -rf $(RELEASE_DIR_NAME)/lib/CVS $(RELEASE_DIR_NAME)/lib/*/CVS
--	if [ -r $(CHARM)/bin/charmd ]; then \
--	  $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \
--	fi
--	if [ -r $(CHARM)/bin/charmd_faceless ]; then \
--	  $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \
--	fi
- 	chmod -R a+rX $(RELEASE_DIR_NAME)
- 	tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME)
- 	gzip $(RELEASE_DIR_NAME).tar
--	echo $(CHARM)
--	ls -l $(CHARM)/lib
- 	-for f in $(RELEASE_FILES); do echo $$f; $(LDD) $$f; done
- 
- winrelease: winall
-Only in NAMD_2.7b2_Source/: Makefile.porig
diff --git a/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch b/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch
deleted file mode 100644
index 40e8e68..0000000
--- a/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-# patch to fix compile error on gcc-3.x
-
-diff -Naur NAMD_2.6b1_Source/src/BackEnd.C NAMD_2.6b1_Source_patched/src/BackEnd.C
---- NAMD_2.6b1_Source/src/BackEnd.C	2003-12-31 06:37:15.000000000 +0000
-+++ NAMD_2.6b1_Source_patched/src/BackEnd.C	2005-08-22 18:59:59.000000000 +0000
-@@ -162,7 +162,7 @@
- }
- 
- // start QD and scheduler
--void BackEnd::barrier(void) {
-+void BackEnd::namd_barrier(void) {
-   awaken();
-   suspend();
- }
-diff -Naur NAMD_2.6b1_Source/src/BackEnd.h NAMD_2.6b1_Source_patched/src/BackEnd.h
---- NAMD_2.6b1_Source/src/BackEnd.h	2000-01-29 00:20:05.000000000 +0000
-+++ NAMD_2.6b1_Source_patched/src/BackEnd.h	2005-08-22 18:59:47.000000000 +0000
-@@ -17,7 +17,7 @@
- 
-   static void suspend(void);  // Let message code run...
-   static void awaken(void);  // ...then return
--  static void barrier(void);  // Let message code run, then return
-+  static void namd_barrier(void);  // Let message code run, then return
-   static void ExitSchedOn(int pe); // Tell a remote processor to stop
-                                    // his scheduler
- 
-diff -Naur NAMD_2.6b1_Source/src/ScriptTcl.C NAMD_2.6b1_Source_patched/src/ScriptTcl.C
---- NAMD_2.6b1_Source/src/ScriptTcl.C	2005-06-23 18:47:00.000000000 +0000
-+++ NAMD_2.6b1_Source_patched/src/ScriptTcl.C	2005-08-22 19:00:21.000000000 +0000
-@@ -56,7 +56,7 @@
- }
- 
- void ScriptTcl::barrier() {
--  BackEnd::barrier();
-+  BackEnd::namd_barrier();
- }
- 
- void ScriptTcl::initcheck() {
-diff -Naur NAMD_2.6b1_Source/src/main.C NAMD_2.6b1_Source_patched/src/main.C
---- NAMD_2.6b1_Source/src/main.C	2005-05-27 22:56:49.000000000 +0000
-+++ NAMD_2.6b1_Source_patched/src/main.C	2005-08-22 19:17:34.000000000 +0000
-@@ -67,7 +67,9 @@
- 
- #ifndef NOHOSTNAME
-   iout << iINFO <<
--     "Sending usage information to NAMD developers via UDP.  Sent data is:\n"
-+     "Markus says: I don't want to send usage information \n" 
-+     << endi;
-+  iout << iINFO << "to NAMD developers :) Data not sent is:\n"
-      << endi;
- 
-   char sendbuf[TBSOFT_TRACK_MAXLEN];
-@@ -88,7 +90,7 @@
-   sprintf(sendbuf, "1 %s  %s  %s  %s  %s  %s  %s", 
-     program, versionnum, platform, numcpus, miscinfo, host, user);
-   iout << iINFO << sendbuf << "\n" << endi;
--  send_dgram(TBSOFT_TRACK_HOST, TBSOFT_TRACK_PORT, sendbuf, strlen(sendbuf));
-+  //send_dgram(TBSOFT_TRACK_HOST, TBSOFT_TRACK_PORT, sendbuf, strlen(sendbuf));
- 
- #endif
-   return 0;
diff --git a/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch b/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch
deleted file mode 100644
index 731ea23..0000000
--- a/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-# adjust paths for proper linking to fftw libs
-
---- NAMD_2.6b1_Source/arch/Linux-i686.fftw	2004-02-20 22:38:36.000000000 +0000
-+++ NAMD_2.6b1_Source_patched/arch/Linux-i686.fftw	2005-08-22 18:50:38.000000000 +0000
-@@ -1,7 +1,7 @@
- 
--FFTDIR=/Projects/namd2/fftw/linux
--FFTINCL=-I$(FFTDIR)/include -I$(HOME)/fftw/include
--FFTLIB=-L$(FFTDIR)/lib -L$(HOME)/fftw/lib -lsrfftw -lsfftw
-+#FFTDIR=/Projects/namd2/fftw/linux
-+FFTINCL=-I/usr/include 
-+FFTLIB=-L/usr/lib -lsrfftw -lsfftw
- FFTFLAGS=-DNAMD_FFTW
- FFT=$(FFTINCL) $(FFTFLAGS)
- 
diff --git a/sci-chemistry/namd/files/namd-makefile-gentoo.patch b/sci-chemistry/namd/files/namd-makefile-gentoo.patch
deleted file mode 100644
index 4ee5822..0000000
--- a/sci-chemistry/namd/files/namd-makefile-gentoo.patch
+++ /dev/null
@@ -1,88 +0,0 @@
-# provide paths for charm++ provided includes/libraries/binaries
-
---- NAMD_2.6b1_Source-patched/Makefile	2005-07-22 18:50:58.000000000 +0000
-+++ NAMD_2.6b1_Source/Makefile	2005-09-30 02:28:35.000000000 +0000
-@@ -227,10 +227,10 @@
- 	$(DSTDIR)/stringhash.o
- 
- # definitions for Charm routines
--CHARMC = $(CHARM)/bin/charmc
--CHARMXI = $(CHARM)/bin/charmc
--CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1
--CHARMLIB = $(CHARM)/lib
-+CHARMC = /usr/bin/charmc
-+CHARMXI = /usr/bin/charmc
-+CHARMINC = /usr/include/charm-5.9 $(COPTD)CMK_OPTIMIZE=1
-+CHARMLIB = /usr/lib
- 
- # Libraries we may have changed
- LIBS = $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL)
-@@ -250,7 +250,7 @@
- 
- # Add new executables here.
- 
--BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb
-+BINARIES = namd2 psfgen flipdcd flipbinpdb
- 
- # This should be rebuilt at every compile, but not on Win32.
- BUILDINFO = $(DSTDIR)/buildinfo
-@@ -279,10 +279,7 @@
- 	$(CHARMOPTS) \
- 	-lm -o namd2
- 
--charmrun: $(CHARM)/bin/charmrun # XXX
--	$(COPY) $(CHARM)/bin/charmrun $@
--
--win32binaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
-+win32binaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe 
- 
- namd2.exe:  $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
- 	$(MAKEBUILDINFO)
-@@ -304,9 +301,6 @@
- charmd_faceless.exe:
- 	$(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
- 
--charmrun.exe:
--	$(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
--
- psfgen:	$(DSTDIR) $(SBOBJS)
- 	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
- 
-@@ -565,9 +559,9 @@
- 
- DOC_FILES = README.txt announce.txt license.txt notes.txt
- 
--RELEASE_FILES = namd2 psfgen charmrun flipdcd flipbinpdb
-+RELEASE_FILES = namd2 psfgen flipdcd flipbinpdb
- 
--WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmrun.exe charmd.exe charmd_faceless.exe $(TCLDLL)
-+WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe $(TCLDLL)
- 
- release: all
- 	$(ECHO) Creating release $(RELEASE_DIR_NAME)
-@@ -575,18 +569,18 @@
- 	cp $(RELEASE_FILES) $(RELEASE_DIR_NAME)
- 	for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done
- 	cp -r .rootdir/lib $(RELEASE_DIR_NAME)
--	if [ -r $(CHARM)/bin/charmd ]; then \
--	  $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \
-+	if [ -r /usr/bin/charmd ]; then \
-+	  $(COPY) /usr/bin/charmd $(RELEASE_DIR_NAME); \
- 	fi
--	if [ -r $(CHARM)/bin/charmd_faceless ]; then \
--	  $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \
-+	if [ -r /usr/bin/charmd_faceless ]; then \
-+	  $(COPY) /usr/bin/charmd_faceless $(RELEASE_DIR_NAME); \
- 	fi
- 	chmod -R a+rX $(RELEASE_DIR_NAME)
- 	tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME)
- 	gzip $(RELEASE_DIR_NAME).tar
--	echo $(CHARM)
--	ls -l $(CHARM)/lib
--	echo $(CHARM)
-+	echo /usr
-+	ls -l /usr/lib
-+	echo /usr
- 	file $(RELEASE_FILES)
- 
- winrelease: winall
diff --git a/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch b/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch
deleted file mode 100644
index 0e6f0dd..0000000
--- a/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-# adjust paths for proper linking to tcl libs 
-
---- NAMD_2.6b1_Source/arch/Linux-i686.tcl	2004-10-27 21:40:55.000000000 +0000
-+++ NAMD_2.6b1_Source_patched/arch/Linux-i686.tcl	2005-09-14 20:50:14.000000000 +0000
-@@ -1,8 +1,8 @@
- 
--TCLDIR=/Projects/namd2/tcl/linux
-+#TCLDIR=/Projects/namd2/tcl/linux
- #TCLDIR=$(HOME)/tcl/cray-xt3
--TCLINCL=-I$(TCLDIR)/include -I$(HOME)/tcl/include
--TCLLIB=-L$(TCLDIR)/lib -L$(HOME)/tcl/lib -ltcl8.3 -ldl
-+TCLINCL=-I/usr/include 
-+TCLLIB=-L/usr/lib -L$(HOME)/tcl/lib -ltcl -ldl
- TCLFLAGS=-DNAMD_TCL -DUSE_NON_CONST
- TCL=$(TCLINCL) $(TCLFLAGS)
- 
diff --git a/sci-chemistry/namd/metadata.xml b/sci-chemistry/namd/metadata.xml
deleted file mode 100644
index dafc7c9..0000000
--- a/sci-chemistry/namd/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-    <maintainer>
-        <email>markusle@gentoo.org</email>
-        <name>Markus Dittrich</name>
-    </maintainer>
-	<herd>sci-chemistry</herd>
-</pkgmetadata>
diff --git a/sci-chemistry/namd/namd-2.7_beta1.ebuild b/sci-chemistry/namd/namd-2.7_beta1.ebuild
deleted file mode 100644
index faadfbc..0000000
--- a/sci-chemistry/namd/namd-2.7_beta1.ebuild
+++ /dev/null
@@ -1,102 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/namd-2.7.ebuild,v 1.2 2009/09/23 19:55:56 patrick Exp $
-
-inherit eutils toolchain-funcs flag-o-matic
-
-DESCRIPTION="A powerful and highly parallelized molecular dynamics code"
-LICENSE="namd"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/"
-
-MY_PN="NAMD"
-MY_PV="2.7b1"
-
-SRC_URI="${MY_PN}_${MY_PV}_Source.tar.gz"
-
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-RESTRICT="fetch"
-
-DEPEND="|| ( app-shells/csh
-			app-shells/tcsh )
-	sys-cluster/charm
-	=sci-libs/fftw-2*
-	dev-lang/tcl"
-
-RDEPEND=${DEPEND}
-
-NAMD_ARCH="Linux-x86_64-g++"
-
-NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD"
-
-S="${WORKDIR}/${MY_PN}_${MY_PV}_Source"
-
-pkg_nofetch() {
-	echo
-	einfo "Please download ${MY_PN}_${MY_PV}_Source.tar.gz from"
-	einfo "${NAMD_DOWNLOAD}"
-	einfo "after agreeing to the license and then move it to"
-	einfo "${DISTDIR}"
-	einfo "Be sure to select the ${MY_PV} version!"
-	echo
-}
-
-src_unpack() {
-	unpack ${A}
-	cd "${WORKDIR}"
-# apply a few small fixes to make NAMD compile and
-	# link to the proper libraries
-	epatch "${FILESDIR}"/namd-2.7-gentoo.patch
-	cd "${S}"
-	# proper compiler and cflags
-	sed -e "s/g++/$(tc-getCXX)/" \
-		-e "s/gcc/$(tc-getCC)/" \
-		-e "s/CXXOPTS = -O3 -m64 -fexpensive-optimizations -ffast-math/CXXOPTS = ${CXXFLAGS}/" \
-		-e "s/COPTS = -O3 -m64 -fexpensive-optimizations -ffast-math/COPTS = ${CFLAGS}/" \
-		-i arch/${NAMD_ARCH}.arch || \
-		die "Failed to setup ${NAMD_ARCH}.arch"
-
-	sed -e "s/gentoo-libdir/$(get_libdir)/g" \
-		-e "s/gentoo-charm/charm-6.1.2/g" \
-		-i Makefile || die "Failed gentooizing Makefile."
-	sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.fftw || \
-		die "Failed gentooizing Linux-x86_64.fftw."
-	sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || \
-		die "Failed gentooizing Linux-x86_64.tcl."
-
-	# configure
-	./config ${NAMD_ARCH}
-}
-
-src_compile() {
-	# build namd
-	cd "${S}/${NAMD_ARCH}"
-	emake || die "Failed to build namd"
-}
-
-src_install() {
-	cd "${S}/${NAMD_ARCH}"
-
-	# the binaries
-	dobin ${PN}2 psfgen flipbinpdb flipdcd || \
-		die "Failed to install binaries"
-
-	cd "${S}"
-
-	# some docs
-	dodoc announce.txt license.txt notes.txt || \
-		die "Failed to install docs"
-}
-
-pkg_postinst() {
-	echo
-	einfo "For detailed instructions on how to run and configure"
-	einfo "NAMD please consults the extensive documentation at"
-	einfo "http://www.ks.uiuc.edu/Research/namd/"
-	einfo "and the NAMD tutorials available at"
-	einfo "http://www.ks.uiuc.edu/Training/Tutorials/"
-	einfo "Have fun :)"
-	echo
-}
diff --git a/sci-chemistry/namd/namd-2.7_beta2.ebuild b/sci-chemistry/namd/namd-2.7_beta2.ebuild
deleted file mode 100644
index dfb23ec..0000000
--- a/sci-chemistry/namd/namd-2.7_beta2.ebuild
+++ /dev/null
@@ -1,110 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/namd-2.7.ebuild,v 1.2 2009/09/23 19:55:56 patrick Exp $
-
-inherit eutils toolchain-funcs flag-o-matic
-
-DESCRIPTION="A powerful and highly parallelized molecular dynamics code"
-LICENSE="namd"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/"
-
-MY_PN="NAMD"
-MY_PV="2.7b2"
-
-SRC_URI="${MY_PN}_${MY_PV}_Source.tar.gz"
-
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-RESTRICT="fetch"
-
-DEPEND="|| ( app-shells/csh
-			app-shells/tcsh )
-	sys-cluster/charm
-	=sci-libs/fftw-2*
-	dev-lang/tcl"
-
-RDEPEND=${DEPEND}
-
-NAMD_ARCH="Linux-x86_64-g++"
-
-NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD"
-
-S="${WORKDIR}/${MY_PN}_${MY_PV}_Source"
-
-pkg_nofetch() {
-	echo
-	einfo "Please download ${MY_PN}_${MY_PV}_Source.tar.gz from"
-	einfo "${NAMD_DOWNLOAD}"
-	einfo "after agreeing to the license and then move it to"
-	einfo "${DISTDIR}"
-	einfo "Be sure to select the ${MY_PV} version!"
-	echo
-}
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	CHARM_VERSION=$(best_version sys-cluster/charm | cut -d- -f3)
-
-	# apply a few small fixes to make NAMD compile and
-	# link to the proper libraries
-	epatch "${FILESDIR}"/namd-2.7_beta2-gentoo.patch
-	sed -e "s:charm-6.1.3:charm-${CHARM_VERSION}:" \
-		Make.charm || \
-		die
-
-	rm -f charm-6.1.3.tar || die
-
-	# proper compiler and cflags
-	sed -e "s/g++/$(tc-getCXX)/" \
-		-e "s/gcc/$(tc-getCC)/" \
-		-e "s/CXXOPTS = -O3 -m64 -fexpensive-optimizations -ffast-math/CXXOPTS = ${CXXFLAGS}/" \
-		-e "s/COPTS = -O3 -m64 -fexpensive-optimizations -ffast-math/COPTS = ${CFLAGS}/" \
-		-i arch/${NAMD_ARCH}.arch || \
-		die "Failed to setup ${NAMD_ARCH}.arch"
-
-	sed -e "s/gentoo-libdir/$(get_libdir)/g" \
-		-e "s/gentoo-charm/charm-${CHARM_VERSION}/g" \
-		-i Makefile || die "Failed gentooizing Makefile."
-	sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.fftw || \
-		die "Failed gentooizing Linux-x86_64.fftw."
-	sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || \
-		die "Failed gentooizing Linux-x86_64.tcl."
-
-	# configure
-	./config ${NAMD_ARCH}
-}
-
-src_compile() {
-	# build namd
-	cd "${S}/${NAMD_ARCH}"
-	emake || die "Failed to build namd"
-}
-
-src_install() {
-	cd "${S}/${NAMD_ARCH}"
-
-	# the binaries
-	dobin ${PN}2 psfgen flipbinpdb flipdcd || \
-		die "Failed to install binaries"
-
-	cd "${S}"
-
-	# some docs
-	dodoc announce.txt license.txt notes.txt || \
-		die "Failed to install docs"
-}
-
-pkg_postinst() {
-	echo
-	einfo "For detailed instructions on how to run and configure"
-	einfo "NAMD please consults the extensive documentation at"
-	einfo "http://www.ks.uiuc.edu/Research/namd/"
-	einfo "and the NAMD tutorials available at"
-	einfo "http://www.ks.uiuc.edu/Training/Tutorials/"
-	einfo "Have fun :)"
-	echo
-}