namd: bump to 2.7 beta 3 for testing.

13 files changed, 805 insertions, 0 deletions

diff --git a/sci-chemistry/namd/ChangeLog b/sci-chemistry/namd/ChangeLog
new file mode 100644
index 0000000..4c3f229
--- /dev/null
+++ b/sci-chemistry/namd/ChangeLog
@@ -0,0 +1,72 @@
+# ChangeLog for sci-chemistry/namd
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/ChangeLog,v 1.13 2010/06/24 20:37:03 jlec Exp $
+
+*namd-2.7_beta2-r1 (24 Jun 2010)
+
+  24 Jun 2010; Justin Lecher <jlec@gentoo.org> namd-2.7_beta2.ebuild,
+  +namd-2.7_beta2-r1.ebuild, +files/namd-2.7-iml-dec.patch,
+  +files/namd-2.7-ldflags.patch:
+  respect LDFLAGS and declarations
+
+  24 Jun 2010; Justin Lecher <jlec@gentoo.org> -namd-2.7_beta1.ebuild:
+  Removed unneeded
+
+*namd-2.7_beta2 (24 Apr 2010)
+*namd-2.7_beta1 (24 Apr 2010)
+
+  24 Apr 2010; Donnie Berkholz <dberkholz@gentoo.org>;
+  +namd-2.7_beta1.ebuild, +namd-2.7_beta2.ebuild, -namd-2.7.ebuild,
+  +files/namd-2.7_beta2-gentoo.patch:
+  Bump to 2.7_beta2. The previous 2.7 ebuild was actually 2.7 beta 1 but was
+  not named as such, so rename it to allow people to upgrade to beta 2.
+
+  23 Apr 2010; Donnie Berkholz <dberkholz@gentoo.org>; namd-2.7.ebuild:
+  All tc-get* sed replacements must happen before C*FLAGS-related ones,
+  otherwise we can replace things like -frecord-gcc-switches with
+  -frecord-x86_64-pc-linux-gnu-gcc-switches.
+
+  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
new file mode 100644
index 0000000..4c39c87
--- /dev/null
+++ b/sci-chemistry/namd/Manifest
@@ -0,0 +1,13 @@
+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-iml-dec.patch 520 RMD160 f8f33d8e10a7c6933369c3a6b857d44243bb1c74 SHA1 2edd740e3b6cb5514bde0c4742d0ca4bf6b98126 SHA256 6be7d0a3b4dff7fa39246e7ce49afb82ff508456ebbe3983e2def1202ebb3024
+AUX namd-2.7-ldflags.patch 1547 RMD160 bfaf2ca893168e1a652e75a186817d8149af94d8 SHA1 a0ce28bcc65e1cb7ff5c61723e602c26f5eef16b SHA256 ce2fd68cf2bf0c459c65caef4e71010b2ae5bf3c2c16770d44ca461291b9b924
+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_2.7b2_Source.tar.gz 9094631 RMD160 ec2c46f6cdb582dca73ebdbd894a9827f2e276d9 SHA1 0acab2a3bb6fca67b767f02bf7d2d2045ce6c3b9 SHA256 5675eb08534a6e4ea7a59e52e949991b3ba42abd78b45a46976ac3d7ed3b8d67
+EBUILD namd-2.7_beta3.ebuild 3019 RMD160 7c6b2d55862b1801a11e76f01a948a877c32f723 SHA1 da5e52329540afb11086ed6622647a5fc61b13bc SHA256 d143385761f8bbee43be726bdfea6c0652757bc446feabe5142f0f4314750474
+MISC ChangeLog 2797 RMD160 050da7ba2120061612df6321b0ffd2e49c1ae9e6 SHA1 06d5dc422168a91e935ebd7d5596f4a474ce0c53 SHA256 05c0e8e730d8ba7cebcd8bb0435aa8980e686b908713cc340c222d0455ad8421
+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
new file mode 100644
index 0000000..9a71de8
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.6-gentoo.patch
@@ -0,0 +1,107 @@
+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
new file mode 100644
index 0000000..733ee8e
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.7-gentoo.patch
@@ -0,0 +1,117 @@
+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-iml-dec.patch b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch
new file mode 100644
index 0000000..e5ee3bd
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch
@@ -0,0 +1,24 @@
+diff --git a/src/flipbinpdb.c b/src/flipbinpdb.c
+index 94b71ba..01a2529 100644
+--- a/src/flipbinpdb.c
++++ b/src/flipbinpdb.c
+@@ -9,6 +9,7 @@
+ #include <sys/mman.h>
+ #include <fcntl.h>
+ #include <stdio.h>
++#include <stdlib.h>
+ 
+ #ifndef MAP_FILE
+ #define MAP_FILE 0
+diff --git a/src/flipdcd.c b/src/flipdcd.c
+index 8ec85b7..1c23433 100644
+--- a/src/flipdcd.c
++++ b/src/flipdcd.c
+@@ -13,6 +13,7 @@
+ #include <sys/mman.h>
+ #include <fcntl.h>
+ #include <stdio.h>
++#include <stdlib.h>
+ 
+ #ifndef MAP_FILE
+ #define MAP_FILE 0
diff --git a/sci-chemistry/namd/files/namd-2.7-ldflags.patch b/sci-chemistry/namd/files/namd-2.7-ldflags.patch
new file mode 100644
index 0000000..686eba8
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.7-ldflags.patch
@@ -0,0 +1,41 @@
+diff --git a/Makefile b/Makefile
+index fd20f12..0821bed 100644
+--- a/Makefile
++++ b/Makefile
+@@ -339,7 +339,7 @@ all:	$(BINARIES) $(LIBCUDARTSO)
+ 
+ namd2:	$(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
+ 	$(MAKEBUILDINFO)
+-	$(CHARMC) -verbose -ld++-option \
++	$(CHARMC) $(LDFLAGS) -verbose -ld++-option \
+ 	"$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \
+ 	-module NeighborLB -module commlib -language charm++ \
+ 	$(BUILDINFO).o \
+@@ -394,23 +394,23 @@ charmrun.exe:
+ 	$(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
+ 
+ psfgen:	$(DSTDIR) $(SBOBJS) $(PLUGINOBJS)
+-	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
++	$(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
+ 
+ psfgen.exe:	$(DSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL)
+ 	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
+ 
+ flipdcd:	$(SRCDIR)/flipdcd.c
+-	$(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \
+ 	echo "#!/bin/sh\necho unavailable on this platform" > $@; \
+ 	chmod +x $@
+ 
+ flipbinpdb:	$(SRCDIR)/flipbinpdb.c
+-	$(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipbinpdb.c || \
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipbinpdb.c || \
+ 	echo "#!/bin/sh\necho unavailable on this platform" > $@; \
+ 	chmod +x $@
+ 
+ fixdcd:	$(SRCDIR)/fixdcd.c
+-	$(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c
+ 
+ dumpdcd:	$(SRCDIR)/dumpdcd.c
+ 	$(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c
diff --git a/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch b/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch
new file mode 100644
index 0000000..898d6b5
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch
@@ -0,0 +1,126 @@
+diff -ur NAMD_2.7b2_Source.orig//arch/Linux-x86_64.fftw NAMD_2.7b2_Source//arch/Linux-x86_64.fftw
+--- NAMD_2.7b2_Source.orig//arch/Linux-x86_64.fftw	2010-04-23 14:40:54.566510874 -0500
++++ NAMD_2.7b2_Source//arch/Linux-x86_64.fftw	2010-04-23 14:41:08.106528893 -0500
+@@ -1,7 +1,7 @@
+ 
+-FFTDIR=/Projects/namd2/fftw/linux-x86_64
++FFTDIR=/usr
+ FFTINCL=-I$(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
new file mode 100644
index 0000000..40e8e68
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch
@@ -0,0 +1,61 @@
+# 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
new file mode 100644
index 0000000..731ea23
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch
@@ -0,0 +1,15 @@
+# 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
new file mode 100644
index 0000000..4ee5822
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-makefile-gentoo.patch
@@ -0,0 +1,88 @@
+# 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 $(RELEASE_FILES)
+ 
+ winrelease: winall
diff --git a/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch b/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch
new file mode 100644
index 0000000..0e6f0dd
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch
@@ -0,0 +1,16 @@
+# adjust paths for proper linking to tcl libs 
+
+--- NAMD_2.6b1_Source/arch/Linux-i686.tcl	2004-10-27 21:40:55.000000000 +0000
++++ NAMD_2.6b1_Source_patched/arch/Linux-i686.tcl	2005-09-14 20:50:14.000000000 +0000
+@@ -1,8 +1,8 @@
+ 
+-TCLDIR=/Projects/namd2/tcl/linux
++#TCLDIR=/Projects/namd2/tcl/linux
+ #TCLDIR=$(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
new file mode 100644
index 0000000..dafc7c9
--- /dev/null
+++ b/sci-chemistry/namd/metadata.xml
@@ -0,0 +1,9 @@
+<?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_beta3.ebuild b/sci-chemistry/namd/namd-2.7_beta3.ebuild
new file mode 100644
index 0000000..f629826
--- /dev/null
+++ b/sci-chemistry/namd/namd-2.7_beta3.ebuild
@@ -0,0 +1,116 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/namd-2.7_beta2-r1.ebuild,v 1.1 2010/06/24 20:37:03 jlec Exp $
+
+inherit eutils toolchain-funcs flag-o-matic multilib
+
+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="cuda"
+
+RESTRICT="fetch"
+
+DEPEND="
+	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
+	epatch "${FILESDIR}"/namd-2.7-ldflags.patch
+	epatch "${FILESDIR}"/namd-2.7-iml-dec.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/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || \
+		die "Failed gentooizing Linux-x86_64.tcl."
+
+	if use cuda; then
+		CONFIG_OPTIONS="--with-cuda --cuda-prefix=/opt/cuda/$(get_libdir)"
+	fi
+
+	# configure
+	./config ${NAMD_ARCH} ${CONFIG_OPTIONS}
+}
+
+src_compile() {
+	# build namd
+	cd "${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
+}