gentoo-overlay/sci-chemistry/namd/files/namd-2.6-gentoo.patch

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)