version bump

Package-Manager: portage-2.2.1/cvs/Linux x86_64
Manifest-Sign-Key: 0xC2000586

5 files changed, 280 insertions, 9 deletions

diff --git a/sci-chemistry/namd/ChangeLog b/sci-chemistry/namd/ChangeLog
index 94d3ef8d53d9..1d33e588c347 100644
--- a/sci-chemistry/namd/ChangeLog
+++ b/sci-chemistry/namd/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/namd
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/ChangeLog,v 1.16 2013/01/11 08:11:06 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/ChangeLog,v 1.17 2013/10/18 16:25:04 ottxor Exp $
+
+*namd-2.9 (18 Oct 2013)
+
+  18 Oct 2013; Christoph Junghans <ottxor@gentoo.org>
+  +files/namd-2.9-gentoo.patch, +namd-2.9.ebuild, metadata.xml:
+  version bump
 
   11 Jan 2013; Justin Lecher <jlec@gentoo.org> files/namd-2.7-gentoo.patch,
   metadata.xml:
@@ -80,4 +86,3 @@
   +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
index bedb78b1453d..a106e93263a4 100644
--- a/sci-chemistry/namd/Manifest
+++ b/sci-chemistry/namd/Manifest
@@ -6,18 +6,25 @@ AUX namd-2.7-gentoo.patch 4043 SHA256 6e2ff2a523c53f5d32e905d6a326d4ca8a4f1de073
 AUX namd-2.7-iml-dec.patch 520 SHA256 6be7d0a3b4dff7fa39246e7ce49afb82ff508456ebbe3983e2def1202ebb3024 SHA512 50ddf91bcb0e370a98d6fe5329f00ec9a8016f0178e342b086f4b9d4130a41e525ed9d960e92dc83b4372f135ce9d454bef836d3e215fb6ac7933999278efa37 WHIRLPOOL f68a4f6bd2df6b8d031ca8709bdb66e6ab558b520ea3ad9bef4ea949e24be6380717c3da9840e8daa9b65cfa8b007d37c36ea0e33f7b4c39ab08f93a4e0ecade
 AUX namd-2.7-ldflags.patch 1547 SHA256 ce2fd68cf2bf0c459c65caef4e71010b2ae5bf3c2c16770d44ca461291b9b924 SHA512 02129638b51703d1be1e9f8ec0e2688201b7709504f5c73a52bf6ab877b12acbcc9056d4f4aaa2b83b5c7df96022de8e4f4b59521bd6d95dd9ebb1cc5a4dde12 WHIRLPOOL 46b0516fa3d591cefcc550b2973fbcf62cfbfc8fea71d2e750b9af249d48d1cf4710d26802dca27b35ecad372764cb374d0666aed9abdc9bc33743156fe22d4a
 AUX namd-2.7_beta2-gentoo.patch 4409 SHA256 c56728dbf426540f9558db31f7e45cacc654112022f42917e715dbaa6c05373d SHA512 0ac58ef97280375eaedd3fe554efe61a8ac12ec0f183bd23308f5186dcc002f6755da959f40c6514150539d8ae2f524af08b3b67b53416e6f96df97664eb6373 WHIRLPOOL 6462f5cda23b812544450b31bc1ca715be5275fbd987083b237b5d03ec79e604ce5dcadf111ea1e82a0cf86906ba969a36e550eab31641b3e7ecd97fadcab719
+AUX namd-2.9-gentoo.patch 5480 SHA256 ff76fceaadbd267023eb30cf256a44aff2b7cd567c8bcf1362afbfec6ca2b26f SHA512 e59a01fe0b65fe9df6b47e962f776eea650b55071081210d0e1269dd76e4da4bca8faef11398bd0cb1f8acc883c8ebf6b37d7fdab066602fd251aae82cb87264 WHIRLPOOL 2b9fee1f2c8a872665b77275b32b45cbd0965aedae5cdaf08024f317add12d57ac93c1f8fc2d91cfb2c8b209cd7fa26e020e2c1a109e667d5b765d79aabcbf26
 AUX namd-barrier-fix-gentoo.patch 2362 SHA256 f0186fada88b387c0681095174be336d61b2968197d223c15c840c1ca96e4992 SHA512 ea01a4a0e42d38867e00b41e46d20a7a708626e7603dbbb647bd18387c72a0da93bf2e34ce372d4f01e8078bcc0573904b3a5c500c879fbd02a76cdc48bd2111 WHIRLPOOL 7736dad2f84255adc6a61104a4e99b39e5cde196c838cb6d3cb3907b7f45fa86f1ebf3b51a846eaf55e710f4fce0a81554ce8a4d04b7240c694e061b2e1d12ee
 AUX namd-fftw-lib-gentoo.patch 528 SHA256 04528fd52f70cccbba1ccf844b97b256a35f9b1b85ca3ef8a56b4c9308b22696 SHA512 27ae0da6c2f1829849d058ae30b8ed8f254fd0c7b8aa6708f4e5f8561211c2d8ec0d0dc8b39cf49ba0ac85422d36fda2cb5d2a889b8254b1d77da26dadd23a35 WHIRLPOOL 3de0f9e2ea958dadc2f6362af9c672872a86e18d555305329c704270f2ad44cd96c4b4231d76061c6e762c45494ebe7576e6bea4da034aba4f0df5744618de78
 AUX namd-makefile-gentoo.patch 2804 SHA256 f3945ae8fff113286847d61a00d5a749b1c3a00b65394085e56ff47a0a209250 SHA512 fcf5f8880267a6738020f9cd5fea3739da8f87fac3a3030f383f883762cdd5e68b75c898d0ddcc6a23f791ddd35d6f60cc4ef6f7d2ce6dbd1709e2fce9a074de WHIRLPOOL 09cc03231626473059a36f33ed7a59688752680a798eebd6ee45990987e1ce8fcd913d4354e3b5ecc0ca63771764ea86c16d42af0118753e4618bc3b21087212
 AUX namd-tcl-lib-gentoo.patch 576 SHA256 7a57497410f5791b1b9fa0535e66137bd1b4c5008e0253c7467bc40af7b6ac01 SHA512 c400437c475165f2e9aa22de3f44aaf21d226ba678cc021d3705b91239159ab702293b3212b5673fcd158e7e42248db1d1984be3bb95256bcca1962c632e9d27 WHIRLPOOL edcfd5dca373f6f040f3dcaab07abb8807989ef5db3cb97fc95307b842afb8af6f964879b7321689f02ad4b81dc087a655b4c2cf322570175ed4ef4878f12ab4
 DIST NAMD_2.7b2_Source.tar.gz 9094631 SHA256 5675eb08534a6e4ea7a59e52e949991b3ba42abd78b45a46976ac3d7ed3b8d67 SHA512 d6906ab8b6dcba42f1021acc59d52e7e3717cb3d236fc64d435f09ee929516fbca2656c8873535683f4a75d390943d67ec102e5192a0eee945f6a4e4bdfd9cf7 WHIRLPOOL 933e4eb50bcf6e9c4d7b06c941c350b33a1d00615fed6ae9c9b656d405ecd443b46cf926f0e9175a3feca6ee9f3e546f212b891fe895c126bcdf94e3e32436eb
+DIST NAMD_2.9_Source.tar.gz 8814042 SHA256 9ba6a1f87d4600a62847728d7c223295be214f9a72b5bb62552f74d644108424 SHA512 0644814a2799b560d9dcf807ba0047325bc9f0a26e3831b0465d95180784f038d69595e036daac85d59cd919c92d11a0343031975d99deb1fa3052c8a649bdd6 WHIRLPOOL 5494ccb2ee2f2792fe52ad7dcfe6da9d11453f0a9b0859d30698dea56b00d92fae73465967f82bd708abee5cd4ff50b0a6ffde86451e859e2f515af203e09286
 EBUILD namd-2.7_beta2-r1.ebuild 2663 SHA256 5664e8d896f4eafa65e76860d283727997bf11c724f92c0d929cc1344fe2a1cc SHA512 edfb25ebe2565e7b1b5770f5fcb0ffd8a8cee00df09eaf4dfcddd440e9d370d866005b8b585129a8f804828986f4ba0aacf77a6f501afd5855596132bc6c52cb WHIRLPOOL d9f09d8146e051b1a5c0430c81d735a346889cef8cd710cbe2aaa16b829836cc200a7ed8d7b3116c4a92aea57dd3f9a11caad30fc607b78e8a68343d84b79667
-MISC ChangeLog 3165 SHA256 5160f26d465f9b631bf57b7d8e382d1676096548e8e92ca41a01954dcadc4d87 SHA512 9ffb5d25df561d62a72e3315ae3e49fa49564eecf8a8a2324a8aa6c3914dd74ed959db6a974c0e872a1b20da9b11baec587a5d784454891ed8785e1f8e761502 WHIRLPOOL a1a73798a5d72790f9d6e2e999db7709f80c083369577319f07ec689d48034433ddb5895654e3524875db7ba4ca9cf22e20d9d5b46742f63ddc53cd23f2b1a14
-MISC metadata.xml 168 SHA256 705462092174cd3e2e3ec1557a28108a746b7351f803d8ca6d1b925b3111c3ff SHA512 f0073fb277e20adb7781aa6ea7f8237bc2d350f0aa43f0f0cca33e02cf52b8fc117bd984c11721ac519a2637ea145976148ac1aba7335dc74c42f7b9531cbed3 WHIRLPOOL 07dd7a302e695440f5033889e5b20cada57beedf17ad33f95d45fb5c39da98bf206eaff13334c20c1c08140a9c5e6041341d29c58efc5ca59b112b60e1662318
+EBUILD namd-2.9.ebuild 2704 SHA256 f42b432b080cf538dc1c40387397b260ccddad04d1b569d844d7334de6d54dc2 SHA512 4960b2b26f1009711adadd29c10b5971cbe5a0e0c4861a28a0b14b52dc4704082c8c50f2f32538f7bcbc75cb7736700b0298a1287d21b7a5233707a1e70d17fd WHIRLPOOL 6758fa1ca6f0d707fc5e5a0571a6d9ca3c4bb5af8f32298765cdc05e176a2a0c6ed0e82bd0548ff2d32bdc4b8ac5595ca206c9ac6e5beb82f094254e0d29c6cc
+MISC ChangeLog 3325 SHA256 eaf53457067f26ff99d24a8c9ad6422327ae39db0c491682508d403750901d8b SHA512 9dc7ca7600a1a81acddcd069333362cb1a3a260a01b27bd63208fbde543bdf967e0c8c6a91dacdfbf67064d15d63e000f2b145b91d89607a4755501d7ab908b5 WHIRLPOOL 65cd4d5a5f21b91cf267b8d0103dd9e220d782df63436d52c2021d44b2754fbecda8c1d2d282af922977c66962ae42e4625950a01870ae4743bbcc26e7f41dc1
+MISC metadata.xml 235 SHA256 d7dc15d73f3f1bc49cc05c9b87c7313dbd0444daa689e93c652a8308faac9fc4 SHA512 54df4839ea6422d861c4d9503aacf9c5222ba2c699b22305e3f5a77869feb9ff6fd95a2447180b9242cfa229563f7c7b083ab2040095510f1fbd689dbe2458b9 WHIRLPOOL 5f38641f262563eb3222fdcab521c5c5ea9beb36d55f7e4e5bc63cc12cea381b25b714736e6109f4899f050cccffb54209d740110be33a36661eb26ed96ce557
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+Version: GnuPG v2.0.22 (GNU/Linux)
 
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diff --git a/sci-chemistry/namd/files/namd-2.9-gentoo.patch b/sci-chemistry/namd/files/namd-2.9-gentoo.patch
new file mode 100644
index 000000000000..583cc52645df
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.9-gentoo.patch
@@ -0,0 +1,151 @@
+diff -Naur NAMD_2.9_Source.original/Make.charm NAMD_2.9_Source/Make.charm
+--- NAMD_2.9_Source.original/Make.charm	2012-02-29 19:12:11.000000000 -0700
++++ NAMD_2.9_Source/Make.charm	2013-09-13 21:23:26.000000000 -0600
+@@ -2,5 +2,5 @@
+ # The config script will override this setting if there is a directory
+ # called charm-6.4.0 or charm in the NAMD base directory.
+ 
+-CHARMBASE = /Projects/namd2/charm-6.4.0
++CHARMBASE = /usr/include/charm-6.4.0
+ 
+diff -Naur NAMD_2.9_Source.original/Makefile NAMD_2.9_Source/Makefile
+--- NAMD_2.9_Source.original/Makefile	2012-04-27 09:53:24.000000000 -0600
++++ NAMD_2.9_Source/Makefile	2013-09-13 21:30:15.000000000 -0600
+@@ -344,10 +344,10 @@
+ 	$(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
+ CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
+ #CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
+ #MSA = -DCHARM_HAS_MSA
+@@ -370,7 +370,7 @@
+ 
+ # Add new executables here.
+ 
+-BINARIES = namd2 psfgen sortreplicas charmrun flipdcd flipbinpdb
++BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb
+ 
+ # This should be rebuilt at every compile, but not on Win32.
+ BUILDINFO = $(DSTDIR)/buildinfo
+@@ -386,7 +386,7 @@
+ 
+ namd2:	$(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS)
+ 	$(MAKEBUILDINFO)
+-	$(CHARMC) -verbose -ld++-option \
++	$(CHARMC) $(LDFLAGS) -verbose -ld++-option \
+ 	"$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \
+ 	"$(CHARM_MODULES)" -language charm++ \
+ 	$(BUILDINFO).o \
+@@ -402,16 +402,9 @@
+ 	$(EXTRALINKLIBS) \
+ 	-lm -o namd2
+ 
+-charmrun: $(CHARM)/bin/charmrun # XXX
+-	$(COPY) $(CHARM)/bin/charmrun $@
+-
+ $(LIBCUDARTSO):
+ 	$(COPY) $(CUDASODIR)/$(LIBCUDARTSO) $@;
+ 
+-WINDOWSBINARIES = namd2.exe psfgen.exe sortreplicas.exe
+-# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
+-windowsbinaries: $(WINDOWSBINARIES)
+-
+ namd2.exe:  $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) $(TCLDLL)
+ 	$(MAKEBUILDINFO)
+ 	$(CHARMC) -verbose \
+@@ -434,11 +427,8 @@
+ charmd_faceless.exe:
+ 	$(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
+ 
+-charmrun.exe:
+-	$(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
+-
+ psfgen:	$(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS)
+-	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
++	$(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
+ 
+ psfgen.exe:	$(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL)
+ 	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
+@@ -456,7 +446,7 @@
+ 	$(CC) $(CFLAGS) -o diffbinpdb $(SRCDIR)/diffbinpdb.c -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 $@
+ 
+@@ -466,7 +456,7 @@
+ 	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
+@@ -665,9 +655,7 @@
+ 
+ DOC_FILES = README.txt announce.txt license.txt notes.txt
+ 
+-RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen charmrun namd2
+-
+-WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(WINDOWSBINARIES) $(TCLDLL)
++RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen namd2
+ 
+ release: all
+ 	$(ECHO) Creating release $(RELEASE_DIR_NAME)
+@@ -678,17 +666,9 @@
+ 	for f in `find $(RELEASE_DIR_NAME)/lib -name CVS`; do \
+ 	  /bin/rm -rf $$f; \
+ 	done
+-	if [ -r $(CHARM)/bin/charmd ]; then \
+-	  $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \
+-	fi
+-	if [ -r $(CHARM)/bin/charmd_faceless ]; then \
+-	  $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \
+-	fi
+ 	chmod -R a+rX $(RELEASE_DIR_NAME)
+ 	tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME)
+ 	gzip $(RELEASE_DIR_NAME).tar
+-	echo $(CHARM)
+-	ls -l $(CHARM)/lib
+ 	-for f in $(RELEASE_FILES); do echo $$f; $(LDD) $(RELEASE_DIR_NAME)/$$f; done
+ 
+ winrelease: winall
+diff -Naur NAMD_2.9_Source.original/arch/Linux-x86_64.fftw NAMD_2.9_Source/arch/Linux-x86_64.fftw
+--- NAMD_2.9_Source.original/arch/Linux-x86_64.fftw	2009-02-21 21:16:04.000000000 -0700
++++ NAMD_2.9_Source/arch/Linux-x86_64.fftw	2013-09-13 20:55:02.000000000 -0600
+@@ -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) $(FFTFLAGS)
+ 
+diff -Naur NAMD_2.9_Source.original/arch/Linux-x86_64.tcl NAMD_2.9_Source/arch/Linux-x86_64.tcl
+--- NAMD_2.9_Source.original/arch/Linux-x86_64.tcl	2011-06-17 14:38:43.000000000 -0600
++++ NAMD_2.9_Source/arch/Linux-x86_64.tcl	2013-09-13 20:56:30.000000000 -0600
+@@ -1,9 +1,9 @@
+ 
+ #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64
+-TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded
++TCLDIR=/usr
+ TCLINCL=-I$(TCLDIR)/include
+ #TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl
+-TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread
++TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl -lpthread
+ TCLFLAGS=-DNAMD_TCL
+ TCL=$(TCLINCL) $(TCLFLAGS)
+ 
diff --git a/sci-chemistry/namd/metadata.xml b/sci-chemistry/namd/metadata.xml
index 51fdedab1b38..34d4431685e4 100644
--- a/sci-chemistry/namd/metadata.xml
+++ b/sci-chemistry/namd/metadata.xml
@@ -1,5 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <herd>sci-chemistry</herd>
+	<herd>sci-chemistry</herd>
+	<maintainer>
+		<email>nicolasbock@gmail.com</email>
+	</maintainer>
 </pkgmetadata>
diff --git a/sci-chemistry/namd/namd-2.9.ebuild b/sci-chemistry/namd/namd-2.9.ebuild
new file mode 100644
index 000000000000..962f6db662c6
--- /dev/null
+++ b/sci-chemistry/namd/namd-2.9.ebuild
@@ -0,0 +1,105 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/namd-2.9.ebuild,v 1.1 2013/10/18 16:25:04 ottxor Exp $
+
+EAPI=5
+
+inherit eutils multilib 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"
+
+SRC_URI="${MY_PN}_${PV}_Source.tar.gz"
+
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+RESTRICT="fetch"
+
+DEPEND="
+	app-shells/tcsh
+	|| ( >=sys-cluster/charm-6.5.1-r2 <=sys-cluster/charm-6.5.1-r1[static-libs] )
+	sci-libs/fftw:2.1
+	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}/${MY_PN}_${PV}_Source"
+
+pkg_nofetch() {
+	echo
+	einfo "Please download ${MY_PN}_${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 ${PV} version!"
+	echo
+}
+
+src_prepare() {
+	CHARM_VERSION=$(best_version sys-cluster/charm | cut -d- -f3)
+
+	# apply a few small fixes to make NAMD compile and
+	# link to the proper libraries
+	epatch "${FILESDIR}"/namd-2.9-gentoo.patch
+	epatch "${FILESDIR}"/namd-2.7-iml-dec.patch
+	sed \
+		-e "s:charm-.\+:charm-${CHARM_VERSION}:" \
+		-i Make.charm || die
+
+	# Remove charm distribution. We don't need it.
+	rm -f charm-6.4.0.tar || die
+
+	# proper compiler and cflags
+	sed \
+		-e "s/g++/$(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
+
+	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/$(get_libdir)/g" -i arch/Linux-x86_64.fftw || die
+	sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || die
+}
+
+src_configure() {
+	# configure
+	./config ${NAMD_ARCH} --charm-arch . || die
+}
+
+src_compile() {
+	# build namd
+	cd "${S}/${NAMD_ARCH}"
+	emake
+}
+
+src_install() {
+	dodoc announce.txt license.txt notes.txt
+	cd "${S}/${NAMD_ARCH}"
+
+	# the binaries
+	dobin ${PN}2 psfgen flipbinpdb flipdcd
+}
+
+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
+}