Attachment #128075 for bug #171971




# Created by: Glenn Johnson
# Date Created:                26 August 1998
# Whom:                        Glenn Johnson
#
# $FreeBSD: ports/biology/tinker/Makefile,v 1.43 2011/10/10 20:17:22 pav Exp $
#

PORTNAME=	tinker
PORTVERSION=	6.0.01
CATEGORIES=	biology
MASTER_SITES=	http://dasher.wustl.edu/tinker/downloads/

MAINTAINER=	ports@FreeBSD.org
COMMENT=	A general purpose molecular modelling package

RESTRICTED=	author requests no distribution except from his FTP site

OPTIONS_DEFINE=	OPTIMIZED_FFLAGS DATA DOCS EXAMPLES
OPTIONS_DEFAULT=DATA
OPTIMIZED_FFLAGS_DESC=	compilation optimizations

WRKSRC=		${WRKDIR}/${PORTNAME}
BUILD_WRKSRC=	${WRKSRC}/source
INSTALL_WRKSRC=	${WRKSRC}/source

USE_FORTRAN=	yes
MAKE_ENV=	HAVE_G2C=yes
MAKEFILE=	${WRKSRC}/make/Makefile
ALL_TARGET=	all listing
INSTALL_TARGET=	rename
MAKE_JOBS_SAFE=	yes

SUB_FILES=	pkg-message

DOCS=		0README *.pdf *.txt
SAMPLES=	0README *.make *.dyn *.int *.frac *.key *.seq *.pdb *.xyz
BENCHES=	0README *.dyn0 *.log *.key *.run *.xyz results*

.include <bsd.port.pre.mk>

.if ${PORT_OPTIONS:MOPTIMIZED_FFLAGS}

.if defined(WITH_OPTIMIZED_FLAGS)
FFLAGS+=	-O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations
.if (${ARCH} == "i386")
FFLAGS+=	-mfancy-math-387 -malign-double
.endif # i386
.endif

.if empty(PORT_OPTIONS:MDATA)
NOPORTDATA=	yes
	@${ECHO_MSG} "You can optimize by setting WITH_OPTIMIZED_FLAGS=yes."
.endif

post-extract:
	@${CHMOD} -R u+w ${WRKSRC}

post-patch:
	@${REINPLACE_CMD} -e 's|%%FFLAGS%%|${FFLAGS}|g' ${WRKSRC}/../make/Makefile

post-install:
	@${MKDIR} ${DATADIR}
	${INSTALL_DATA} ${INSTALL_WRKSRC}/tinker.txt ${DATADIR}
	@${MKDIR} ${DATADIR}/params
	${INSTALL_DATA} ${WRKSRC}/params/* ${DATADIR}/params
.if ${PORT_OPTIONS:MDATA}
	@${INSTALL_DATA} ${WRKDIR}/tinker/params/* \
		${DATADIR}/params
.if !defined(NOPORTDOCS)
	@${MKDIR} ${DOCSDIR}
	@${MKDIR} ${EXAMPLESDIR}
	@${MKDIR} ${DATADIR}/bench
	${INSTALL_DATA} ${BENCHES:S|^|${WRKSRC}/bench/|} ${DATADIR}/bench
	@${MKDIR} ${DATADIR}/test
	${INSTALL_DATA} ${WRKSRC}/test/* ${DATADIR}/test
.endif
.if ${PORT_OPTIONS:MDOCS}
	@${MKDIR} ${DOCSDIR}
	${INSTALL_DATA} ${DOCS:S|^|${WRKSRC}/doc/|} ${DOCSDIR}
.endif
.if ${PORT_OPTIONS:MEXAMPLES}
	@${MKDIR} ${EXAMPLESDIR}
	${INSTALL_DATA} ${SAMPLES:S|^|${WRKSRC}/example/|} ${EXAMPLESDIR}
.endif
	@${ECHO_CMD}
	@${CAT} ${PKGMESSAGE}
	@${ECHO_CMD}
	@${ECHO_MSG} "       to him if you find Tinker to be useful.               "
	@${ECHO_MSG} "                                                             "
	@${ECHO_MSG} "       See ${DOCSDIR} for license forms.     "
	@${ECHO_MSG} "   **********************************************************"
	@${ECHO_MSG} ""

.include <bsd.port.post.mk>

Lines 1-2 Link Here

(-)biology/tinker/distinfo (-2 / +2 lines)
1	SHA256 (tinker-5.1.09.tar.gz) = 61765adfe260e3f3083243542dac49d38141191d5d6580e9a66a29c31d5a3183	1	SHA256 (tinker-6.0.01.tar.gz) = 98f4ffdec889944e5bbe10196ac2c9a7888a3708db3998027ffc65cb6e39dd71
2	SIZE (tinker-5.1.09.tar.gz) = 14071638	2	SIZE (tinker-6.0.01.tar.gz) = 18093304




--- ../make/Makefile.orig	2010-08-25 00:58:16.000000000 +0400
+++ ../make/Makefile	2011-01-22 01:12:41.000000000 +0300
@@ -9,8 +9,8 @@
 ##
 ##   1. make all              Build all the TINKER executables
 ##   2. make rename           Move the executables to BINDIR
-##   3. make remove_links     Create soft links in LINKDIR
-##   4. make create_links     Remove soft links from LINKDIR
+##   3. make remove_links     Remove soft links in LINKDIR
+##   4. make create_links     Create soft links from LINKDIR
 ##   6. make listing          Concatenate source to tinker.txt
 ##   5. make clean            Delete objects and executables
 ##
@@ -30,9 +30,9 @@
 ##  LINKDIR      Linked Copies of TINKER Executables
 ##
 
-TINKERDIR = /Users/ponder/tinker
-BINDIR = $(TINKERDIR)/bin
-LINKDIR = /usr/local/bin
+TINKERDIR = ${WRKDIR}
+BINDIR = ${PREFIX}/bin
+#LINKDIR = /usr/local/bin
 
 ####################################################################
 ##  Known Machine Types; Uncomment One of the Following Sections  ##
@@ -40,6 +40,20 @@
 ####################################################################
 
 ##
+##  Machine:  IntelPC / FreeBSD
+##  CPU Type: Intel, AMD, Cyrix
+##  Oper Sys: FreeBSD 4.2
+##  Compiler: f77 , aka g77
+##
+
+F77 = ${FC}
+LIBS =
+F77FLAGS = -c %%FFLAGS%%
+LINKFLAGS =
+OPTFLAGS = 
+LIBFLAGS = -rcuv
+
+##
 ##  Machine:  Generic Linux
 ##  CPU Type: Intel x86 Compatible
 ##  Oper Sys: Fedora Core
@@ -102,12 +116,12 @@
 ##  Compiler: Intel Fortran for Mac 11
 ##
 
-F77 = /opt/intel/Compiler/11.1/058/bin/intel64/ifort
-LIBS =
-F77FLAGS = -c -axSSSE3 -vec-report0
-OPTFLAGS = -O3 -no-ipo -no-prec-div
-LIBFLAGS = -crusv
-LINKFLAGS = -static-intel -mmacosx-version-min=10.4
+#F77 = /opt/intel/Compiler/11.1/058/bin/intel64/ifort
+#LIBS =
+#F77FLAGS = -c -axSSSE3 -vec-report0
+#OPTFLAGS = -O3 -no-ipo -no-prec-div
+#LIBFLAGS = -crusv
+#LINKFLAGS = -static-intel -mmacosx-version-min=10.4
 
 ##
 ##  Machine:  Macintosh (PPC)
@@ -584,6 +598,8 @@
            xyzpdb.x \
            xyzsybyl.x
 
+.SUFFIXES: .x
+
 .f.o:
 	${F77} ${F77FLAGS} ${OPTFLAGS} $*.f 
 
@@ -596,8 +612,8 @@
 server.o:
 	${F77} ${F77FLAGS} ${OPTFLAGS} server.f
 
-%.x: %.o libtinker.a
-	${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}
+.o.x: libtinker.a
+	${F77} ${LINKFLAGS} -o $@ $< libtinker.a ${LIBS}
 
 all:	${EXEFILES}
 
@@ -608,63 +624,63 @@
 	cat *.i *.f > tinker.txt
 
 rename:
-	mv  alchemy.x    $(BINDIR)/alchemy
-	mv  analyze.x    $(BINDIR)/analyze
-	mv  anneal.x     $(BINDIR)/anneal
-	mv  archive.x    $(BINDIR)/archive
-	mv  correlate.x  $(BINDIR)/correlate
-	mv  crystal.x    $(BINDIR)/crystal
-	mv  diffuse.x    $(BINDIR)/diffuse
-	mv  distgeom.x   $(BINDIR)/distgeom
-	mv  document.x   $(BINDIR)/document
-	mv  dynamic.x    $(BINDIR)/dynamic
-	mv  gda.x        $(BINDIR)/gda
-	mv  intedit.x    $(BINDIR)/intedit
-	mv  intxyz.x     $(BINDIR)/intxyz
-	mv  minimize.x   $(BINDIR)/minimize
-	mv  minirot.x    $(BINDIR)/minirot
-	mv  minrigid.x   $(BINDIR)/minrigid
-	mv  monte.x      $(BINDIR)/monte
-	mv  newton.x     $(BINDIR)/newton
-	mv  newtrot.x    $(BINDIR)/newtrot
-	mv  nucleic.x    $(BINDIR)/nucleic
-	mv  optimize.x   $(BINDIR)/optimize
-	mv  optirot.x    $(BINDIR)/optirot
-	mv  optrigid.x   $(BINDIR)/optrigid
-	mv  path.x       $(BINDIR)/path
-	mv  pdbxyz.x     $(BINDIR)/pdbxyz
-	mv  polarize.x   $(BINDIR)/polarize
-	mv  poledit.x    $(BINDIR)/poledit
-	mv  potential.x  $(BINDIR)/potential
-	mv  prmedit.x    $(BINDIR)/prmedit
-	mv  protein.x    $(BINDIR)/protein
-	mv  pss.x        $(BINDIR)/pss
-	mv  pssrigid.x   $(BINDIR)/pssrigid
-	mv  pssrot.x     $(BINDIR)/pssrot
-	mv  radial.x     $(BINDIR)/radial
-	mv  saddle.x     $(BINDIR)/saddle
-	mv  scan.x       $(BINDIR)/scan
-	mv  sniffer.x    $(BINDIR)/sniffer
-	mv  spacefill.x  $(BINDIR)/spacefill
-	mv  spectrum.x   $(BINDIR)/spectrum
-	mv  superpose.x  $(BINDIR)/superpose
-	mv  sybylxyz.x   $(BINDIR)/sybylxyz
-	mv  testgrad.x   $(BINDIR)/testgrad
-	mv  testhess.x   $(BINDIR)/testhess
-	mv  testpair.x   $(BINDIR)/testpair
-	mv  testrot.x    $(BINDIR)/testrot
-	mv  timer.x      $(BINDIR)/timer
-	mv  timerot.x    $(BINDIR)/timerot
-	mv  valence.x    $(BINDIR)/valence
-	mv  vibbig.x     $(BINDIR)/vibbig
-	mv  vibrate.x    $(BINDIR)/vibrate
-	mv  vibrot.x     $(BINDIR)/vibrot
-	mv  xtalfit.x    $(BINDIR)/xtalfit
-	mv  xtalmin.x    $(BINDIR)/xtalmin
-	mv  xyzedit.x    $(BINDIR)/xyzedit
-	mv  xyzint.x     $(BINDIR)/xyzint
-	mv  xyzpdb.x     $(BINDIR)/xyzpdb
-	mv  xyzsybyl.x   $(BINDIR)/xyzsybyl
+	${INSTALL_PROGRAM}  alchemy.x    $(BINDIR)/alchemy
+	${INSTALL_PROGRAM}  analyze.x    $(BINDIR)/analyze
+	${INSTALL_PROGRAM}  anneal.x     $(BINDIR)/anneal
+	${INSTALL_PROGRAM}  archive.x    $(BINDIR)/archive
+	${INSTALL_PROGRAM}  correlate.x  $(BINDIR)/correlate
+	${INSTALL_PROGRAM}  crystal.x    $(BINDIR)/crystal
+	${INSTALL_PROGRAM}  diffuse.x    $(BINDIR)/diffuse
+	${INSTALL_PROGRAM}  distgeom.x   $(BINDIR)/distgeom
+	${INSTALL_PROGRAM}  document.x   $(BINDIR)/document
+	${INSTALL_PROGRAM}  dynamic.x    $(BINDIR)/dynamic
+	${INSTALL_PROGRAM}  gda.x        $(BINDIR)/gda
+	${INSTALL_PROGRAM}  intedit.x    $(BINDIR)/intedit
+	${INSTALL_PROGRAM}  intxyz.x     $(BINDIR)/intxyz
+	${INSTALL_PROGRAM}  minimize.x   $(BINDIR)/minimize
+	${INSTALL_PROGRAM}  minirot.x    $(BINDIR)/minirot
+	${INSTALL_PROGRAM}  minrigid.x   $(BINDIR)/minrigid
+	${INSTALL_PROGRAM}  monte.x      $(BINDIR)/monte
+	${INSTALL_PROGRAM}  newton.x     $(BINDIR)/newton
+	${INSTALL_PROGRAM}  newtrot.x    $(BINDIR)/newtrot
+	${INSTALL_PROGRAM}  nucleic.x    $(BINDIR)/nucleic
+	${INSTALL_PROGRAM}  optimize.x   $(BINDIR)/optimize
+	${INSTALL_PROGRAM}  optirot.x    $(BINDIR)/optirot
+	${INSTALL_PROGRAM}  optrigid.x   $(BINDIR)/optrigid
+	${INSTALL_PROGRAM}  path.x       $(BINDIR)/path
+	${INSTALL_PROGRAM}  pdbxyz.x     $(BINDIR)/pdbxyz
+	${INSTALL_PROGRAM}  polarize.x   $(BINDIR)/polarize
+	${INSTALL_PROGRAM}  poledit.x    $(BINDIR)/poledit
+	${INSTALL_PROGRAM}  potential.x  $(BINDIR)/potential
+	${INSTALL_PROGRAM}  prmedit.x    $(BINDIR)/prmedit
+	${INSTALL_PROGRAM}  protein.x    $(BINDIR)/protein
+	${INSTALL_PROGRAM}  pss.x        $(BINDIR)/pss
+	${INSTALL_PROGRAM}  pssrigid.x   $(BINDIR)/pssrigid
+	${INSTALL_PROGRAM}  pssrot.x     $(BINDIR)/pssrot
+	${INSTALL_PROGRAM}  radial.x     $(BINDIR)/radial
+	${INSTALL_PROGRAM}  saddle.x     $(BINDIR)/saddle
+	${INSTALL_PROGRAM}  scan.x       $(BINDIR)/scan
+	${INSTALL_PROGRAM}  sniffer.x    $(BINDIR)/sniffer
+	${INSTALL_PROGRAM}  spacefill.x  $(BINDIR)/spacefill
+	${INSTALL_PROGRAM}  spectrum.x   $(BINDIR)/spectrum
+	${INSTALL_PROGRAM}  superpose.x  $(BINDIR)/superpose
+	${INSTALL_PROGRAM}  sybylxyz.x   $(BINDIR)/sybylxyz
+	${INSTALL_PROGRAM}  testgrad.x   $(BINDIR)/testgrad
+	${INSTALL_PROGRAM}  testhess.x   $(BINDIR)/testhess
+	${INSTALL_PROGRAM}  testpair.x   $(BINDIR)/testpair
+	${INSTALL_PROGRAM}  testrot.x    $(BINDIR)/testrot
+	${INSTALL_PROGRAM}  timer.x      $(BINDIR)/timer
+	${INSTALL_PROGRAM}  timerot.x    $(BINDIR)/timerot
+	${INSTALL_PROGRAM}  valence.x    $(BINDIR)/valence
+	${INSTALL_PROGRAM}  vibbig.x     $(BINDIR)/vibbig
+	${INSTALL_PROGRAM}  vibrate.x    $(BINDIR)/vibrate
+	${INSTALL_PROGRAM}  vibrot.x     $(BINDIR)/vibrot
+	${INSTALL_PROGRAM}  xtalfit.x    $(BINDIR)/xtalfit
+	${INSTALL_PROGRAM}  xtalmin.x    $(BINDIR)/xtalmin
+	${INSTALL_PROGRAM}  xyzedit.x    $(BINDIR)/xyzedit
+	${INSTALL_PROGRAM}  xyzint.x     $(BINDIR)/xyzint
+	${INSTALL_PROGRAM}  xyzpdb.x     $(BINDIR)/xyzpdb
+	${INSTALL_PROGRAM}  xyzsybyl.x   $(BINDIR)/xyzsybyl
 
 remove_links:
 	rm -f $(LINKDIR)/alchemy

Lines 1-5 Link Here

(-)biology/tinker/files/patch-ah (-5 lines)
1	--- ../bench/bench1.run.orig Tue Jul 24 14:02:20 2001
2	+++ ../bench/bench1.run Wed Sep 5 13:57:02 2001
3	@@ -1 +1 @@
4	-../bin/timer bench1 1 y
5	+timer bench1 1 y

Lines 1-5 Link Here

(-)biology/tinker/files/patch-ai (-5 lines)
1	--- ../bench/bench2.run.orig Tue Jul 24 14:02:20 2001
2	+++ ../bench/bench2.run Wed Sep 5 13:58:47 2001
3	@@ -1 +1 @@
4	-../bin/timer bench2 1 y
5	+timer bench2 1 y

Lines 1-5 Link Here

(-)biology/tinker/files/patch-aj (-5 lines)
1	--- ../bench/bench3.run.orig Wed Sep 5 14:00:09 2001
2	+++ ../bench/bench3.run Wed Sep 5 14:01:27 2001
3	@@ -1 +1 @@
4	-time ../bin/vibrate bench3 0
5	+time vibrate bench3 0

Lines 1-7 Link Here

(-)biology/tinker/files/patch-ak (-7 lines)
1	--- ../bench/bench4.run.orig Tue Jul 24 14:02:20 2001
2	+++ ../bench/bench4.run Wed Sep 5 14:02:17 2001
3	@@ -1,3 +1,3 @@
4	cp bench4.dyn0 bench4.dyn
5	-time ../bin/dynamic bench4 1000 1.0 10.0 2 298.0
6	+time dynamic bench4 1000 1.0 10.0 2 298.0
7	rm bench4.dyn

Lines 1-7 Link Here

(-)biology/tinker/files/patch-al (-7 lines)
1	--- ../bench/bench5.run.orig 2010-08-25 00:58:15.000000000 +0400
2	+++ ../bench/bench5.run 2011-01-26 23:35:18.000000000 +0300
3	@@ -1,3 +1,3 @@
4	cp bench5.dyn0 bench5.dyn
5	-time ../bin/dynamic bench5 1000 1.0 10.0 2 298.0
6	+time dynamic bench5 1000 1.0 10.0 2 298.0
7	rm bench5.dyn

Line 0 Link Here

(-)biology/tinker/files/patch-bench__bench1.run (+5 lines)
	1	--- bench/bench1.run.orig Tue Jul 24 14:02:20 2001
	2	+++ bench/bench1.run Wed Sep 5 13:57:02 2001
	3	@@ -1 +1 @@
	4	-../bin/timer bench1 1 y
	5	+timer bench1 1 y

Line 0 Link Here

(-)biology/tinker/files/patch-bench__bench2.run (+5 lines)
	1	--- bench/bench2.run.orig Tue Jul 24 14:02:20 2001
	2	+++ bench/bench2.run Wed Sep 5 13:58:47 2001
	3	@@ -1 +1 @@
	4	-../bin/timer bench2 1 y
	5	+timer bench2 1 y

Line 0 Link Here

(-)biology/tinker/files/patch-bench__bench3.run (+5 lines)
	1	--- bench/bench3.run.orig Wed Sep 5 14:00:09 2001
	2	+++ bench/bench3.run Wed Sep 5 14:01:27 2001
	3	@@ -1 +1 @@
	4	-time ../bin/vibrate bench3 0
	5	+time vibrate bench3 0

Line 0 Link Here

(-)biology/tinker/files/patch-bench__bench4.run (+7 lines)
	1	--- bench/bench4.run.orig Tue Jul 24 14:02:20 2001
	2	+++ bench/bench4.run Wed Sep 5 14:02:17 2001
	3	@@ -1,3 +1,3 @@
	4	cp bench4.dyn0 bench4.dyn
	5	-time ../bin/dynamic bench4 1000 1.0 10.0 2 298.0
	6	+time dynamic bench4 1000 1.0 10.0 2 298.0
	7	rm bench4.dyn

Line 0 Link Here

(-)biology/tinker/files/patch-bench__bench5.run (+7 lines)
	1	--- bench/bench5.run.orig 2010-08-25 00:58:15.000000000 +0400
	2	+++ bench/bench5.run 2011-01-26 23:35:18.000000000 +0300
	3	@@ -1,3 +1,3 @@
	4	cp bench5.dyn0 bench5.dyn
	5	-time ../bin/dynamic bench5 1000 1.0 10.0 2 298.0
	6	+time dynamic bench5 1000 1.0 10.0 2 298.0
	7	rm bench5.dyn




--- make/Makefile.orig	2011-11-06 05:29:19.000000000 +0900
+++ make/Makefile	2011-11-23 05:37:09.000000000 +0900
@@ -9,8 +9,8 @@
 ##
 ##   1. make all              Build all the TINKER executables
 ##   2. make rename           Move the executables to BINDIR
-##   3. make remove_links     Create soft links in LINKDIR
-##   4. make create_links     Remove soft links from LINKDIR
+##   3. make remove_links     Remove soft links in LINKDIR
+##   4. make create_links     Create soft links from LINKDIR
 ##   6. make listing          Concatenate source to tinker.txt
 ##   5. make clean            Delete objects and executables
 ##
@@ -30,9 +30,9 @@
 ##  LINKDIR      Linked Copies of TINKER Executables
 ##
 
-TINKERDIR = /Users/ponder/tinker
-BINDIR = $(TINKERDIR)/bin
-LINKDIR = /usr/local/bin
+TINKERDIR = ${WRKDIR}
+BINDIR = ${PREFIX}/bin
+#LINKDIR = /usr/local/bin
 
 ####################################################################
 ##  Known Machine Types; Uncomment One of the Following Sections  ##
@@ -40,6 +40,20 @@
 ####################################################################
 
 ##
+##  Machine:  IntelPC / FreeBSD
+##  CPU Type: Intel, AMD, Cyrix
+##  Oper Sys: FreeBSD 4.2
+##  Compiler: f77 , aka g77
+##
+
+F77 = ${FC}
+LIBS =
+F77FLAGS = -c ${FFLAGS}
+LINKFLAGS =
+OPTFLAGS = 
+LIBFLAGS = -rcuv
+
+##
 ##  Machine:  Generic Linux
 ##  CPU Type: Intel x86 Compatible
 ##  Oper Sys: Fedora Core
@@ -104,12 +118,12 @@
 ##  Parallel: OpenMP
 ##
 
-F77 = /opt/intel/bin/ifort
-LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_threads -lfftw3
-F77FLAGS = -c -axSSSE3 -assume cc_omp
-OPTFLAGS = -O3 -no-ipo -no-prec-div -openmp
-LIBFLAGS = -crusv
-LINKFLAGS = $(OPTFLAGS) -static-intel -mmacosx-version-min=10.4
+#F77 = /opt/intel/bin/ifort
+#LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_threads -lfftw3
+#F77FLAGS = -c -axSSSE3 -assume cc_omp
+#OPTFLAGS = -O3 -no-ipo -no-prec-div -openmp
+#LIBFLAGS = -crusv
+#LINKFLAGS = $(OPTFLAGS) -static-intel -mmacosx-version-min=10.4
 
 ##
 ##  Machine:  Macintosh
@@ -587,6 +601,8 @@
            xyzpdb.x \
            xyzsybyl.x
 
+.SUFFIXES: .x
+
 .f.o:
 	${F77} ${F77FLAGS} ${OPTFLAGS} $*.f 
 
@@ -596,8 +612,8 @@
 server.o:
 	${F77} ${F77FLAGS} ${OPTFLAGS} server.f
 
-%.x: %.o libtinker.a
-	${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}; strip $@
+.o.x: libtinker.a
+	${F77} ${LINKFLAGS} -o $@ $< libtinker.a ${LIBS}
 
 all:	${EXEFILES}
 
@@ -608,64 +624,64 @@
 	cat *.i *.f *.c > tinker.txt
 
 rename:
-	mv  alchemy.x    $(BINDIR)/alchemy
-	mv  analyze.x    $(BINDIR)/analyze
-	mv  anneal.x     $(BINDIR)/anneal
-	mv  archive.x    $(BINDIR)/archive
-	mv  correlate.x  $(BINDIR)/correlate
-	mv  crystal.x    $(BINDIR)/crystal
-	mv  diffuse.x    $(BINDIR)/diffuse
-	mv  distgeom.x   $(BINDIR)/distgeom
-	mv  document.x   $(BINDIR)/document
-	mv  dynamic.x    $(BINDIR)/dynamic
-	mv  gda.x        $(BINDIR)/gda
-	mv  intedit.x    $(BINDIR)/intedit
-	mv  intxyz.x     $(BINDIR)/intxyz
-	mv  minimize.x   $(BINDIR)/minimize
-	mv  minirot.x    $(BINDIR)/minirot
-	mv  minrigid.x   $(BINDIR)/minrigid
-	mv  monte.x      $(BINDIR)/monte
-	mv  newton.x     $(BINDIR)/newton
-	mv  newtrot.x    $(BINDIR)/newtrot
-	mv  nucleic.x    $(BINDIR)/nucleic
-	mv  optimize.x   $(BINDIR)/optimize
-	mv  optirot.x    $(BINDIR)/optirot
-	mv  optrigid.x   $(BINDIR)/optrigid
-	mv  path.x       $(BINDIR)/path
-	mv  pdbxyz.x     $(BINDIR)/pdbxyz
-	mv  polarize.x   $(BINDIR)/polarize
-	mv  poledit.x    $(BINDIR)/poledit
-	mv  potential.x  $(BINDIR)/potential
-	mv  prmedit.x    $(BINDIR)/prmedit
-	mv  protein.x    $(BINDIR)/protein
-	mv  pss.x        $(BINDIR)/pss
-	mv  pssrigid.x   $(BINDIR)/pssrigid
-	mv  pssrot.x     $(BINDIR)/pssrot
-	mv  radial.x     $(BINDIR)/radial
-	mv  saddle.x     $(BINDIR)/saddle
-	mv  scan.x       $(BINDIR)/scan
-	mv  sniffer.x    $(BINDIR)/sniffer
-	mv  spacefill.x  $(BINDIR)/spacefill
-	mv  spectrum.x   $(BINDIR)/spectrum
-	mv  superpose.x  $(BINDIR)/superpose
-	mv  sybylxyz.x   $(BINDIR)/sybylxyz
-	mv  testgrad.x   $(BINDIR)/testgrad
-	mv  testhess.x   $(BINDIR)/testhess
-	mv  testpair.x   $(BINDIR)/testpair
-	mv  testrot.x    $(BINDIR)/testrot
-	mv  timer.x      $(BINDIR)/timer
-	mv  timerot.x    $(BINDIR)/timerot
-	mv  torsfit.x    $(BINDIR)/torsfit
-	mv  valence.x    $(BINDIR)/valence
-	mv  vibbig.x     $(BINDIR)/vibbig
-	mv  vibrate.x    $(BINDIR)/vibrate
-	mv  vibrot.x     $(BINDIR)/vibrot
-	mv  xtalfit.x    $(BINDIR)/xtalfit
-	mv  xtalmin.x    $(BINDIR)/xtalmin
-	mv  xyzedit.x    $(BINDIR)/xyzedit
-	mv  xyzint.x     $(BINDIR)/xyzint
-	mv  xyzpdb.x     $(BINDIR)/xyzpdb
-	mv  xyzsybyl.x   $(BINDIR)/xyzsybyl
+	${BSD_INSTALL_PROGRAM}  alchemy.x    $(BINDIR)/alchemy
+	${BSD_INSTALL_PROGRAM}  analyze.x    $(BINDIR)/analyze
+	${BSD_INSTALL_PROGRAM}  anneal.x     $(BINDIR)/anneal
+	${BSD_INSTALL_PROGRAM}  archive.x    $(BINDIR)/archive
+	${BSD_INSTALL_PROGRAM}  correlate.x  $(BINDIR)/correlate
+	${BSD_INSTALL_PROGRAM}  crystal.x    $(BINDIR)/crystal
+	${BSD_INSTALL_PROGRAM}  diffuse.x    $(BINDIR)/diffuse
+	${BSD_INSTALL_PROGRAM}  distgeom.x   $(BINDIR)/distgeom
+	${BSD_INSTALL_PROGRAM}  document.x   $(BINDIR)/document
+	${BSD_INSTALL_PROGRAM}  dynamic.x    $(BINDIR)/dynamic
+	${BSD_INSTALL_PROGRAM}  gda.x        $(BINDIR)/gda
+	${BSD_INSTALL_PROGRAM}  intedit.x    $(BINDIR)/intedit
+	${BSD_INSTALL_PROGRAM}  intxyz.x     $(BINDIR)/intxyz
+	${BSD_INSTALL_PROGRAM}  minimize.x   $(BINDIR)/minimize
+	${BSD_INSTALL_PROGRAM}  minirot.x    $(BINDIR)/minirot
+	${BSD_INSTALL_PROGRAM}  minrigid.x   $(BINDIR)/minrigid
+	${BSD_INSTALL_PROGRAM}  monte.x      $(BINDIR)/monte
+	${BSD_INSTALL_PROGRAM}  newton.x     $(BINDIR)/newton
+	${BSD_INSTALL_PROGRAM}  newtrot.x    $(BINDIR)/newtrot
+	${BSD_INSTALL_PROGRAM}  nucleic.x    $(BINDIR)/nucleic
+	${BSD_INSTALL_PROGRAM}  optimize.x   $(BINDIR)/optimize
+	${BSD_INSTALL_PROGRAM}  optirot.x    $(BINDIR)/optirot
+	${BSD_INSTALL_PROGRAM}  optrigid.x   $(BINDIR)/optrigid
+	${BSD_INSTALL_PROGRAM}  path.x       $(BINDIR)/path
+	${BSD_INSTALL_PROGRAM}  pdbxyz.x     $(BINDIR)/pdbxyz
+	${BSD_INSTALL_PROGRAM}  polarize.x   $(BINDIR)/polarize
+	${BSD_INSTALL_PROGRAM}  poledit.x    $(BINDIR)/poledit
+	${BSD_INSTALL_PROGRAM}  potential.x  $(BINDIR)/potential
+	${BSD_INSTALL_PROGRAM}  prmedit.x    $(BINDIR)/prmedit
+	${BSD_INSTALL_PROGRAM}  protein.x    $(BINDIR)/protein
+	${BSD_INSTALL_PROGRAM}  pss.x        $(BINDIR)/pss
+	${BSD_INSTALL_PROGRAM}  pssrigid.x   $(BINDIR)/pssrigid
+	${BSD_INSTALL_PROGRAM}  pssrot.x     $(BINDIR)/pssrot
+	${BSD_INSTALL_PROGRAM}  radial.x     $(BINDIR)/radial
+	${BSD_INSTALL_PROGRAM}  saddle.x     $(BINDIR)/saddle
+	${BSD_INSTALL_PROGRAM}  scan.x       $(BINDIR)/scan
+	${BSD_INSTALL_PROGRAM}  sniffer.x    $(BINDIR)/sniffer
+	${BSD_INSTALL_PROGRAM}  spacefill.x  $(BINDIR)/spacefill
+	${BSD_INSTALL_PROGRAM}  spectrum.x   $(BINDIR)/spectrum
+	${BSD_INSTALL_PROGRAM}  superpose.x  $(BINDIR)/superpose
+	${BSD_INSTALL_PROGRAM}  sybylxyz.x   $(BINDIR)/sybylxyz
+	${BSD_INSTALL_PROGRAM}  testgrad.x   $(BINDIR)/testgrad
+	${BSD_INSTALL_PROGRAM}  testhess.x   $(BINDIR)/testhess
+	${BSD_INSTALL_PROGRAM}  testpair.x   $(BINDIR)/testpair
+	${BSD_INSTALL_PROGRAM}  testrot.x    $(BINDIR)/testrot
+	${BSD_INSTALL_PROGRAM}  timer.x      $(BINDIR)/timer
+	${BSD_INSTALL_PROGRAM}  timerot.x    $(BINDIR)/timerot
+	${BSD_INSTALL_PROGRAM}  torsfit.x    $(BINDIR)/torsfit
+	${BSD_INSTALL_PROGRAM}  valence.x    $(BINDIR)/valence
+	${BSD_INSTALL_PROGRAM}  vibbig.x     $(BINDIR)/vibbig
+	${BSD_INSTALL_PROGRAM}  vibrate.x    $(BINDIR)/vibrate
+	${BSD_INSTALL_PROGRAM}  vibrot.x     $(BINDIR)/vibrot
+	${BSD_INSTALL_PROGRAM}  xtalfit.x    $(BINDIR)/xtalfit
+	${BSD_INSTALL_PROGRAM}  xtalmin.x    $(BINDIR)/xtalmin
+	${BSD_INSTALL_PROGRAM}  xyzedit.x    $(BINDIR)/xyzedit
+	${BSD_INSTALL_PROGRAM}  xyzint.x     $(BINDIR)/xyzint
+	${BSD_INSTALL_PROGRAM}  xyzpdb.x     $(BINDIR)/xyzpdb
+	${BSD_INSTALL_PROGRAM}  xyzsybyl.x   $(BINDIR)/xyzsybyl
 
 remove_links:
 	rm -f $(LINKDIR)/alchemy

Lines 1-8 Link Here

(-)biology/tinker/files/patch-openend.f (-2 / +2 lines)
1		1
2	$FreeBSD: ports/biology/tinker/files/patch-openend.f,v 1.2 2003/07/25 02:48:05 maho Exp $	2	$FreeBSD: ports/biology/tinker/files/patch-openend.f,v 1.2 2003/07/25 02:48:05 maho Exp $
3		3
4	--- openend.f.orig Fri Apr 18 13:31:51 2003	4	--- source/openend.f.orig Fri Apr 18 13:31:51 2003
5	+++ openend.f Mon Jul 21 13:36:11 2003	5	+++ source/openend.f Mon Jul 21 13:36:11 2003
6	@@ -29,11 +29,11 @@	6	@@ -29,11 +29,11 @@
7	c	7	c
8	c standard Fortran 90, unavailable in some Fortran 77 compilers	8	c standard Fortran 90, unavailable in some Fortran 77 compilers

Line 0 Link Here

(-)biology/tinker/files/pkg-message.in (+6 lines)
	1	**********************************************************
	2	The author requests that you return a license form
	3	to him if you find Tinker to be useful.
	4
	5	See %%DOCSDIR%% for license forms.
	6	**********************************************************"




bin/testrot
bin/timer
bin/timerot
bin/torsfit
bin/valence
bin/vibbig
bin/vibrate

%%PORTDOCS%%%%DOCSDIR%%/guide.txt
%%PORTDOCS%%%%DOCSDIR%%/license.pdf
%%PORTDOCS%%%%DOCSDIR%%/license.txt
%%PORTDOCS%%%%DOCSDIR%%/release-3.2
%%PORTDOCS%%%%DOCSDIR%%/release-3.6
%%PORTDOCS%%%%DOCSDIR%%/release-3.7
%%PORTDOCS%%%%DOCSDIR%%/release-3.8
%%PORTDOCS%%%%DOCSDIR%%/release-3.9
%%PORTDOCS%%%%DOCSDIR%%/release-4.0
%%PORTDOCS%%%%DOCSDIR%%/release-4.1
%%PORTDOCS%%%%DOCSDIR%%/release-4.2
%%PORTDOCS%%%%DOCSDIR%%/summary.pdf
%%PORTDOCS%%%%DOCSDIR%%/summary.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/0README
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alatet.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alatet.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alatet.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alatet.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alkane.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alkane.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ammonia.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ammonia.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/amoeba.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/amoeba.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/arach.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/arach.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/arach.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/azulene.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/azulene.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/azulene.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bdna.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bdna.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bdna.make
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bdna.pdb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bdna.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bdna.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bearing.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bearing.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bearing2.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzamidine.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzamidine.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzbox.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzbox.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzene.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzene.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzene.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl2.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl2.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl3.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl3.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bucky.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bucky.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bucky.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane2.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane2.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane2.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanes.dyn
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanes.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanes.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanex.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanex.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls2.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls2.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls2.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c5.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c5.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c5.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c5.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7a.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7a.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7a.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7a.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7e.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7e.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7e.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7e.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/calmodulin.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/calmodulin.pdb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/calmodulin.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/calmodulin.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cawater.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cawater.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/copper.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/copper.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cpentene.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cpentene.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.pdb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambinx.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambinx.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crown.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crown.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crown.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cychept.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cychept.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cychept.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo2.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo2.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo2.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cycprop.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cycprop.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dang.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dang.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.make
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr2.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr2.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr2.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/diamond.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/diamond.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/diene.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/diene.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/diene.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dimethane.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dimethane.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dmp.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dmp.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/enkephalin.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/enkephalin.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/enkephalin.make
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/enkephalin.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/enkephalin.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ermer.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ermer.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ermer.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ester.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ester.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethane.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethane.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethane.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethanol.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethanol.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethanol.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ether.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ether.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/etherbox.dyn
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/etherbox.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/etherbox.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethylene.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethylene.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethylene.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/flane.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/flane.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/flane.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/form.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/form.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/formbig.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/formbig.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/formbox.dyn
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/formbox.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/formbox.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/formopls.dyn
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/formopls.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/formopls.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/furan.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/furan.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/furan.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/glucose.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/glucose.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/glycerol.dyn
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/glycerol.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/glycerol.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/graphite.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/graphite.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/helix.dyn
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/helix.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/helix.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/heme.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/heme.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hexane.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hexane.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hexane.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hexanes.dyn
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hexanes.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hexanes.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/imidazole.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/imidazole.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/imidazole.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/imine.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/imine.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/imine.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/indole.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/indole.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lactam.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lactam.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lipid.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lipid.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lj38.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lj38.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/melittin.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/melittin.pdb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/melittin.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/melittin.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/membrane.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/membrane.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/meohbox.dyn
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/meohbox.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/meohbox.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/methanol.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/methanol.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgwater.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgwater.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mm3.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mm3.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nacl.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nacl.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nada.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nada.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/naphthalene.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/naphthalene.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/naphthalene.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/naphthax.frac
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/naphthax.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/naphthax.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nitrile.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nitrile.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nitrogen.dyn
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nitrogen.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nitrogen.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nma.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nma.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nma.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nmabox.dyn
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nmabox.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nmabox.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nmf.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nmf.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nstilbene.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nstilbene.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nstilbene.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/octane.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/octane.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/octane.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/octane2.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/octane2.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/octane2.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/octene.dyn
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/octene.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/octene.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/palmitate.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/palmitate.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/palmitate.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pentane.frac
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pentane.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pentane.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/peptide.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/peptide.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/peptide.make
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/peptide.pdb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/peptide.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/peptide.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/phenanth.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/phenanth.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/photo.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/photo.pdb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/photo.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/photo.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pol3.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pol3.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/polyala.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/polyala.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/propane.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/propane.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/propellane.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/propellane.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/propellane.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/propyne.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/propyne.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pyridine.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pyridine.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pyridine.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pyrrole.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pyrrole.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pyrrole.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/retinoic.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/retinoic.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/skunk.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/skunk.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/spc.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/spc.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sterol.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sterol.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/styrene.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/styrene.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/styrene.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/terphenyl.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/terphenyl.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tfe.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tfe.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/thiadiene.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/thiadiene.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/thiadiene.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/thiophene.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/thiophene.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/thiophene.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/thr.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/thr.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/thr.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip3f.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip3f.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip3p.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip3p.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip4f.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip4f.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip4p.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip4p.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip5p.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip5p.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/trpcage.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/trpcage.pdb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/trpcage.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/trpcage.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin.pdb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin2.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin2.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin2.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/urea.frac
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/urea.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/urea.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/water.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/water.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/water.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterball.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterball.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterbig.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterbig.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterbox.dyn
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterbox.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterbox.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterdot.dyn
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterdot.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterdot.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterglobe.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterglobe.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterhuge.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterhuge.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterslab.dyn
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterslab.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterslab.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/watersmall.dyn
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/watersmall.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/watersmall.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/watertiny.dyn
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/watertiny.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/watertiny.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/white.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/white.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/white.xyz
%%PORTDATA%%%%DATADIR%%/bench/0README
%%PORTDATA%%%%DATADIR%%/bench/bench1.key
%%PORTDATA%%%%DATADIR%%/bench/bench1.run
%%PORTDATA%%%%DATADIR%%/bench/bench1.xyz
%%PORTDATA%%%%DATADIR%%/bench/bench2.key
%%PORTDATA%%%%DATADIR%%/bench/bench2.run
%%PORTDATA%%%%DATADIR%%/bench/bench2.xyz
%%PORTDATA%%%%DATADIR%%/bench/bench3.key
%%PORTDATA%%%%DATADIR%%/bench/bench3.run
%%PORTDATA%%%%DATADIR%%/bench/bench3.xyz
%%PORTDATA%%%%DATADIR%%/bench/bench4.dyn0
%%PORTDATA%%%%DATADIR%%/bench/bench4.key
%%PORTDATA%%%%DATADIR%%/bench/bench4.log
%%PORTDATA%%%%DATADIR%%/bench/bench4.run
%%PORTDATA%%%%DATADIR%%/bench/bench4.xyz
%%PORTDATA%%%%DATADIR%%/bench/bench5.dyn0
%%PORTDATA%%%%DATADIR%%/bench/bench5.key
%%PORTDATA%%%%DATADIR%%/bench/bench5.log
%%PORTDATA%%%%DATADIR%%/bench/bench5.run
%%PORTDATA%%%%DATADIR%%/bench/bench5.xyz
%%PORTDATA%%%%DATADIR%%/bench/bench6.key
%%PORTDATA%%%%DATADIR%%/bench/bench6.log
%%PORTDATA%%%%DATADIR%%/bench/bench6.run
%%PORTDATA%%%%DATADIR%%/bench/bench6.xyz
%%PORTDATA%%%%DATADIR%%/bench/bench7.key
%%PORTDATA%%%%DATADIR%%/bench/bench7.log
%%PORTDATA%%%%DATADIR%%/bench/bench7.run
%%PORTDATA%%%%DATADIR%%/bench/bench7.xyz
%%PORTDATA%%%%DATADIR%%/bench/results-2.3
%%PORTDATA%%%%DATADIR%%/bench/results-2.4
%%PORTDATA%%%%DATADIR%%/bench/results-2.9
%%PORTDATA%%%%DATADIR%%/bench/results-3.1
%%PORTDATA%%%%DATADIR%%/bench/results-3.2
%%PORTDATA%%%%DATADIR%%/bench/results-3.4
%%PORTDATA%%%%DATADIR%%/bench/results-3.5
%%PORTDATA%%%%DATADIR%%/bench/results-3.7
%%PORTDATA%%%%DATADIR%%/bench/results-3.8
%%PORTDATA%%%%DATADIR%%/bench/results-3.9
%%PORTDATA%%%%DATADIR%%/bench/results-4.0
%%PORTDATA%%%%DATADIR%%/bench/results-4.1
%%PORTDATA%%%%DATADIR%%/bench/results-4.2
%%PORTDATA%%%%DATADIR%%/bench/results-4.3
%%PORTDATA%%%%DATADIR%%/bench/results-5.0
%%PORTDATA%%%%DATADIR%%/bench/results-5.1
%%PORTDATA%%%%DATADIR%%/bench/results-6.0
%%DATADIR%%/params/0README
%%DATADIR%%/params/amber02.prm
%%DATADIR%%/params/amber94.prm
%%DATADIR%%/params/amber96.prm
%%DATADIR%%/params/amber98.prm

%%DATADIR%%/params/smoothua.prm
%%DATADIR%%/params/tiny.prm
%%DATADIR%%/params/water.prm
%%PORTDATA%%%%DATADIR%%/test/0README
%%PORTDATA%%%%DATADIR%%/test/anion.dat
%%PORTDATA%%%%DATADIR%%/test/anion.dyn0
%%PORTDATA%%%%DATADIR%%/test/anion.key
%%PORTDATA%%%%DATADIR%%/test/anion.log
%%PORTDATA%%%%DATADIR%%/test/anion.run
%%PORTDATA%%%%DATADIR%%/test/anion.xyz
%%PORTDATA%%%%DATADIR%%/test/argon.1st
%%PORTDATA%%%%DATADIR%%/test/argon.key
%%PORTDATA%%%%DATADIR%%/test/argon.log
%%PORTDATA%%%%DATADIR%%/test/argon.run
%%PORTDATA%%%%DATADIR%%/test/clean.make
%%PORTDATA%%%%DATADIR%%/test/cluster.dat
%%PORTDATA%%%%DATADIR%%/test/cluster.key
%%PORTDATA%%%%DATADIR%%/test/cluster.log
%%PORTDATA%%%%DATADIR%%/test/cluster.run
%%PORTDATA%%%%DATADIR%%/test/cluster.xyz
%%PORTDATA%%%%DATADIR%%/test/crambin.key
%%PORTDATA%%%%DATADIR%%/test/crambin.log
%%PORTDATA%%%%DATADIR%%/test/crambin.pdb
%%PORTDATA%%%%DATADIR%%/test/crambin.run
%%PORTDATA%%%%DATADIR%%/test/cyclohex.boat
%%PORTDATA%%%%DATADIR%%/test/cyclohex.chair
%%PORTDATA%%%%DATADIR%%/test/cyclohex.key
%%PORTDATA%%%%DATADIR%%/test/cyclohex.log
%%PORTDATA%%%%DATADIR%%/test/cyclohex.run
%%PORTDATA%%%%DATADIR%%/test/dhfr.dyn
%%PORTDATA%%%%DATADIR%%/test/dhfr.key
%%PORTDATA%%%%DATADIR%%/test/dhfr.log
%%PORTDATA%%%%DATADIR%%/test/dhfr.run
%%PORTDATA%%%%DATADIR%%/test/dhfr.xyz
%%PORTDATA%%%%DATADIR%%/test/dialanine.key
%%PORTDATA%%%%DATADIR%%/test/dialanine.log
%%PORTDATA%%%%DATADIR%%/test/dialanine.run
%%PORTDATA%%%%DATADIR%%/test/dialanine.xyz
%%PORTDATA%%%%DATADIR%%/test/enkephalin.dat
%%PORTDATA%%%%DATADIR%%/test/enkephalin.key
%%PORTDATA%%%%DATADIR%%/test/enkephalin.log
%%PORTDATA%%%%DATADIR%%/test/enkephalin.run
%%PORTDATA%%%%DATADIR%%/test/ethanol.000
%%PORTDATA%%%%DATADIR%%/test/ethanol.020
%%PORTDATA%%%%DATADIR%%/test/ethanol.040
%%PORTDATA%%%%DATADIR%%/test/ethanol.060
%%PORTDATA%%%%DATADIR%%/test/ethanol.080
%%PORTDATA%%%%DATADIR%%/test/ethanol.100
%%PORTDATA%%%%DATADIR%%/test/ethanol.120
%%PORTDATA%%%%DATADIR%%/test/ethanol.140
%%PORTDATA%%%%DATADIR%%/test/ethanol.160
%%PORTDATA%%%%DATADIR%%/test/ethanol.180
%%PORTDATA%%%%DATADIR%%/test/ethanol.dat
%%PORTDATA%%%%DATADIR%%/test/ethanol.key
%%PORTDATA%%%%DATADIR%%/test/ethanol.log
%%PORTDATA%%%%DATADIR%%/test/ethanol.run
%%PORTDATA%%%%DATADIR%%/test/ethanol.xyz
%%PORTDATA%%%%DATADIR%%/test/formamide.cell
%%PORTDATA%%%%DATADIR%%/test/formamide.dat
%%PORTDATA%%%%DATADIR%%/test/formamide.key
%%PORTDATA%%%%DATADIR%%/test/formamide.log
%%PORTDATA%%%%DATADIR%%/test/formamide.run
%%PORTDATA%%%%DATADIR%%/test/gpcr.blk
%%PORTDATA%%%%DATADIR%%/test/gpcr.key
%%PORTDATA%%%%DATADIR%%/test/gpcr.log
%%PORTDATA%%%%DATADIR%%/test/gpcr.run
%%PORTDATA%%%%DATADIR%%/test/gpcr.xyz
%%PORTDATA%%%%DATADIR%%/test/helix.1st
%%PORTDATA%%%%DATADIR%%/test/helix.key
%%PORTDATA%%%%DATADIR%%/test/helix.log
%%PORTDATA%%%%DATADIR%%/test/helix.run
%%PORTDATA%%%%DATADIR%%/test/salt.cell
%%PORTDATA%%%%DATADIR%%/test/salt.key
%%PORTDATA%%%%DATADIR%%/test/salt.log
%%PORTDATA%%%%DATADIR%%/test/salt.run
%%PORTDATA%%%%DATADIR%%/test/tetraala.dat
%%PORTDATA%%%%DATADIR%%/test/tetraala.key
%%PORTDATA%%%%DATADIR%%/test/tetraala.log
%%PORTDATA%%%%DATADIR%%/test/tetraala.run
%%PORTDATA%%%%DATADIR%%/test/water.key
%%PORTDATA%%%%DATADIR%%/test/water.log
%%PORTDATA%%%%DATADIR%%/test/water.pot
%%PORTDATA%%%%DATADIR%%/test/water.run
%%PORTDATA%%%%DATADIR%%/test/water.xyz
%%DATADIR%%/tinker.txt
%%PORTDATA%%@dirrm %%DATADIR%%/test
@dirrm %%DATADIR%%/params
%%PORTDATA%%@dirrm %%DATADIR%%/bench
@dirrm %%DATADIR%%
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
%%PORTDOCS%%@dirrm %%DOCSDIR%%

Return to bug 171971

Lines 1-76 Link Here

(-)biology/tinker/Makefile (-41 / +39 lines)
1	# New ports collection makefile for: tinker	1	# Created by: Glenn Johnson
2	# Date Created: 26 August 1998
3	# Whom: Glenn Johnson
4	#
5	# $FreeBSD: ports/biology/tinker/Makefile,v 1.43 2011/10/10 20:17:22 pav Exp $	2	# $FreeBSD: ports/biology/tinker/Makefile,v 1.43 2011/10/10 20:17:22 pav Exp $
6	#
7		3
8	PORTNAME= tinker	4	PORTNAME= tinker
9	PORTVERSION= 5.1.09	5	PORTVERSION= 6.0.01
10	CATEGORIES= biology	6	CATEGORIES= biology
11	MASTER_SITES= http://dasher.wustl.edu/tinker/downloads/	7	MASTER_SITES= http://dasher.wustl.edu/tinker/downloads/
12		8
13	MAINTAINER= ports@FreeBSD.org	9	MAINTAINER= ports@FreeBSD.org
14	COMMENT= A general purpose molecular modelling package	10	COMMENT= A general purpose molecular modelling package
15		11
16	MAKE_ENV+= HAVE_G2C=yes INSTALL_PROGRAM="${INSTALL_PROGRAM}"	12	RESTRICTED= author requests no distribution except from his FTP site
17		13
18	WRKSRC= ${WRKDIR}/tinker/source	14	OPTIONS_DEFINE= OPTIMIZED_FFLAGS DATA DOCS EXAMPLES
		15	OPTIONS_DEFAULT=DATA
		16	OPTIMIZED_FFLAGS_DESC= compilation optimizations
		17
		18	WRKSRC= ${WRKDIR}/${PORTNAME}
		19	BUILD_WRKSRC= ${WRKSRC}/source
		20	INSTALL_WRKSRC= ${WRKSRC}/source
19		21
20	MAKEFILE= ${WRKDIR}/tinker/make/Makefile	22	USE_FORTRAN= yes
		23	MAKE_ENV= HAVE_G2C=yes
		24	MAKEFILE= ${WRKSRC}/make/Makefile
21	ALL_TARGET= all listing	25	ALL_TARGET= all listing
22	INSTALL_TARGET= rename	26	INSTALL_TARGET= rename
23	RESTRICTED= author requests no distribution except from his FTP site	27	MAKE_JOBS_SAFE= yes
		28
		29	SUB_FILES= pkg-message
24		30
25	DOCS= 0README .pdf .txt announce/release*	31	DOCS= 0README .pdf .txt
26	SAMPLES= 0README .make .dyn .int .frac .key .seq .pdb .run *.xyz	32	SAMPLES= 0README .make .dyn .int .frac .key .seq .pdb .xyz
27	BENCHES= 0README .dyn0 .log .key .run .xyz results	33	BENCHES= 0README .dyn0 .log .key .run .xyz results
28		34
29	.include <bsd.port.pre.mk>	35	.include <bsd.port.pre.mk>
30		36
31	USE_FORTRAN= yes	37	.if ${PORT_OPTIONS:MOPTIMIZED_FFLAGS}
32
33	.if defined(WITH_OPTIMIZED_FLAGS)
34	FFLAGS+= -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations	38	FFLAGS+= -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations
35	.if (${ARCH} == "i386")	39	.if (${ARCH} == "i386")
36	FFLAGS+= -mfancy-math-387 -malign-double	40	FFLAGS+= -mfancy-math-387 -malign-double
37	.endif # i386	41	.endif # i386
38	.endif	42	.endif
39		43
40	pre-everything::	44	.if empty(PORT_OPTIONS:MDATA)
41	.if !defined(WITH_OPTIMIZED_FLAGS)	45	NOPORTDATA= yes
42	@${ECHO_MSG} "You can optimize by setting WITH_OPTIMIZED_FLAGS=yes."
43	.endif	46	.endif
44		47
45	post-extract:	48	post-extract:
46	${CHMOD} -R u+w ${WRKDIR}/tinker	49	@${CHMOD} -R u+w ${WRKSRC}
47
48	post-patch:
49	@${REINPLACE_CMD} -e 's\|%%FFLAGS%%\|${FFLAGS}\|g' ${WRKSRC}/../make/Makefile
50		50
51	post-install:	51	post-install:
		52	@${MKDIR} ${DATADIR}
		53	${INSTALL_DATA} ${INSTALL_WRKSRC}/tinker.txt ${DATADIR}
52	@${MKDIR} ${DATADIR}/params	54	@${MKDIR} ${DATADIR}/params
53	@${INSTALL_DATA} ${WRKDIR}/tinker/source/tinker.txt \	55	${INSTALL_DATA} ${WRKSRC}/params/* ${DATADIR}/params
54	${DATADIR}	56	.if ${PORT_OPTIONS:MDATA}
55	@${INSTALL_DATA} ${WRKDIR}/tinker/params/* \
56	${DATADIR}/params
57	.if !defined(NOPORTDOCS)
58	@${MKDIR} ${DOCSDIR}
59	@${MKDIR} ${EXAMPLESDIR}
60	@${MKDIR} ${DATADIR}/bench	57	@${MKDIR} ${DATADIR}/bench
		58	${INSTALL_DATA} ${BENCHES:S\|^\|${WRKSRC}/bench/\|} ${DATADIR}/bench
61	@${MKDIR} ${DATADIR}/test	59	@${MKDIR} ${DATADIR}/test
62	@${INSTALL_DATA} ${DOCS:S\|^\|${WRKDIR}/tinker/doc/\|} ${DOCSDIR}	60	${INSTALL_DATA} ${WRKSRC}/test/* ${DATADIR}/test
63	@${INSTALL_DATA} ${SAMPLES:S\|^\|${WRKDIR}/tinker/example/\|} ${EXAMPLESDIR}	61	.endif
64	@${INSTALL_DATA} ${BENCHES:S\|^\|${WRKDIR}/tinker/bench/\|} ${DATADIR}/bench	62	.if ${PORT_OPTIONS:MDOCS}
65	@${INSTALL_DATA} ${WRKDIR}/tinker/test/* ${DATADIR}/test	63	@${MKDIR} ${DOCSDIR}
		64	${INSTALL_DATA} ${DOCS:S\|^\|${WRKSRC}/doc/\|} ${DOCSDIR}
		65	.endif
		66	.if ${PORT_OPTIONS:MEXAMPLES}
		67	@${MKDIR} ${EXAMPLESDIR}
		68	${INSTALL_DATA} ${SAMPLES:S\|^\|${WRKSRC}/example/\|} ${EXAMPLESDIR}
66	.endif	69	.endif
67	@${ECHO_MSG} ""	70	@${ECHO_CMD}
68	@${ECHO_MSG} " **********************************************************"	71	@${CAT} ${PKGMESSAGE}
69	@${ECHO_MSG} " The author requests that you return a license form "	72	@${ECHO_CMD}
70	@${ECHO_MSG} " to him if you find Tinker to be useful. "
71	@${ECHO_MSG} " "
72	@${ECHO_MSG} " See ${DOCSDIR} for license forms. "
73	@${ECHO_MSG} " **********************************************************"
74	@${ECHO_MSG} ""
75		73
76	.include <bsd.port.post.mk>	74	.include <bsd.port.post.mk>

Lines 1-207 Link Here

(-)biology/tinker/files/patch-aa (-207 lines)
1	--- ../make/Makefile.orig 2010-08-25 00:58:16.000000000 +0400
2	+++ ../make/Makefile 2011-01-22 01:12:41.000000000 +0300
3	@@ -9,8 +9,8 @@
4	##
5	## 1. make all Build all the TINKER executables
6	## 2. make rename Move the executables to BINDIR
7	-## 3. make remove_links Create soft links in LINKDIR
8	-## 4. make create_links Remove soft links from LINKDIR
9	+## 3. make remove_links Remove soft links in LINKDIR
10	+## 4. make create_links Create soft links from LINKDIR
11	## 6. make listing Concatenate source to tinker.txt
12	## 5. make clean Delete objects and executables
13	##
14	@@ -30,9 +30,9 @@
15	## LINKDIR Linked Copies of TINKER Executables
16	##
17
18	-TINKERDIR = /Users/ponder/tinker
19	-BINDIR = $(TINKERDIR)/bin
20	-LINKDIR = /usr/local/bin
21	+TINKERDIR = ${WRKDIR}
22	+BINDIR = ${PREFIX}/bin
23	+#LINKDIR = /usr/local/bin
24
25	####################################################################
26	## Known Machine Types; Uncomment One of the Following Sections ##
27	@@ -40,6 +40,20 @@
28	####################################################################
29
30	##
31	+## Machine: IntelPC / FreeBSD
32	+## CPU Type: Intel, AMD, Cyrix
33	+## Oper Sys: FreeBSD 4.2
34	+## Compiler: f77 , aka g77
35	+##
36	+
37	+F77 = ${FC}
38	+LIBS =
39	+F77FLAGS = -c %%FFLAGS%%
40	+LINKFLAGS =
41	+OPTFLAGS =
42	+LIBFLAGS = -rcuv
43	+
44	+##
45	## Machine: Generic Linux
46	## CPU Type: Intel x86 Compatible
47	## Oper Sys: Fedora Core
48	@@ -102,12 +116,12 @@
49	## Compiler: Intel Fortran for Mac 11
50	##
51
52	-F77 = /opt/intel/Compiler/11.1/058/bin/intel64/ifort
53	-LIBS =
54	-F77FLAGS = -c -axSSSE3 -vec-report0
55	-OPTFLAGS = -O3 -no-ipo -no-prec-div
56	-LIBFLAGS = -crusv
57	-LINKFLAGS = -static-intel -mmacosx-version-min=10.4
58	+#F77 = /opt/intel/Compiler/11.1/058/bin/intel64/ifort
59	+#LIBS =
60	+#F77FLAGS = -c -axSSSE3 -vec-report0
61	+#OPTFLAGS = -O3 -no-ipo -no-prec-div
62	+#LIBFLAGS = -crusv
63	+#LINKFLAGS = -static-intel -mmacosx-version-min=10.4
64
65	##
66	## Machine: Macintosh (PPC)
67	@@ -584,6 +598,8 @@
68	xyzpdb.x \
69	xyzsybyl.x
70
71	+.SUFFIXES: .x
72	+
73	.f.o:
74	${F77} ${F77FLAGS} ${OPTFLAGS} $*.f
75
76	@@ -596,8 +612,8 @@
77	server.o:
78	${F77} ${F77FLAGS} ${OPTFLAGS} server.f
79
80	-%.x: %.o libtinker.a
81	- ${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}
82	+.o.x: libtinker.a
83	+ ${F77} ${LINKFLAGS} -o $@ $< libtinker.a ${LIBS}
84
85	all: ${EXEFILES}
86
87	@@ -608,63 +624,63 @@
88	cat .i .f > tinker.txt
89
90	rename:
91	- mv alchemy.x $(BINDIR)/alchemy
92	- mv analyze.x $(BINDIR)/analyze
93	- mv anneal.x $(BINDIR)/anneal
94	- mv archive.x $(BINDIR)/archive
95	- mv correlate.x $(BINDIR)/correlate
96	- mv crystal.x $(BINDIR)/crystal
97	- mv diffuse.x $(BINDIR)/diffuse
98	- mv distgeom.x $(BINDIR)/distgeom
99	- mv document.x $(BINDIR)/document
100	- mv dynamic.x $(BINDIR)/dynamic
101	- mv gda.x $(BINDIR)/gda
102	- mv intedit.x $(BINDIR)/intedit
103	- mv intxyz.x $(BINDIR)/intxyz
104	- mv minimize.x $(BINDIR)/minimize
105	- mv minirot.x $(BINDIR)/minirot
106	- mv minrigid.x $(BINDIR)/minrigid
107	- mv monte.x $(BINDIR)/monte
108	- mv newton.x $(BINDIR)/newton
109	- mv newtrot.x $(BINDIR)/newtrot
110	- mv nucleic.x $(BINDIR)/nucleic
111	- mv optimize.x $(BINDIR)/optimize
112	- mv optirot.x $(BINDIR)/optirot
113	- mv optrigid.x $(BINDIR)/optrigid
114	- mv path.x $(BINDIR)/path
115	- mv pdbxyz.x $(BINDIR)/pdbxyz
116	- mv polarize.x $(BINDIR)/polarize
117	- mv poledit.x $(BINDIR)/poledit
118	- mv potential.x $(BINDIR)/potential
119	- mv prmedit.x $(BINDIR)/prmedit
120	- mv protein.x $(BINDIR)/protein
121	- mv pss.x $(BINDIR)/pss
122	- mv pssrigid.x $(BINDIR)/pssrigid
123	- mv pssrot.x $(BINDIR)/pssrot
124	- mv radial.x $(BINDIR)/radial
125	- mv saddle.x $(BINDIR)/saddle
126	- mv scan.x $(BINDIR)/scan
127	- mv sniffer.x $(BINDIR)/sniffer
128	- mv spacefill.x $(BINDIR)/spacefill
129	- mv spectrum.x $(BINDIR)/spectrum
130	- mv superpose.x $(BINDIR)/superpose
131	- mv sybylxyz.x $(BINDIR)/sybylxyz
132	- mv testgrad.x $(BINDIR)/testgrad
133	- mv testhess.x $(BINDIR)/testhess
134	- mv testpair.x $(BINDIR)/testpair
135	- mv testrot.x $(BINDIR)/testrot
136	- mv timer.x $(BINDIR)/timer
137	- mv timerot.x $(BINDIR)/timerot
138	- mv valence.x $(BINDIR)/valence
139	- mv vibbig.x $(BINDIR)/vibbig
140	- mv vibrate.x $(BINDIR)/vibrate
141	- mv vibrot.x $(BINDIR)/vibrot
142	- mv xtalfit.x $(BINDIR)/xtalfit
143	- mv xtalmin.x $(BINDIR)/xtalmin
144	- mv xyzedit.x $(BINDIR)/xyzedit
145	- mv xyzint.x $(BINDIR)/xyzint
146	- mv xyzpdb.x $(BINDIR)/xyzpdb
147	- mv xyzsybyl.x $(BINDIR)/xyzsybyl
148	+ ${INSTALL_PROGRAM} alchemy.x $(BINDIR)/alchemy
149	+ ${INSTALL_PROGRAM} analyze.x $(BINDIR)/analyze
150	+ ${INSTALL_PROGRAM} anneal.x $(BINDIR)/anneal
151	+ ${INSTALL_PROGRAM} archive.x $(BINDIR)/archive
152	+ ${INSTALL_PROGRAM} correlate.x $(BINDIR)/correlate
153	+ ${INSTALL_PROGRAM} crystal.x $(BINDIR)/crystal
154	+ ${INSTALL_PROGRAM} diffuse.x $(BINDIR)/diffuse
155	+ ${INSTALL_PROGRAM} distgeom.x $(BINDIR)/distgeom
156	+ ${INSTALL_PROGRAM} document.x $(BINDIR)/document
157	+ ${INSTALL_PROGRAM} dynamic.x $(BINDIR)/dynamic
158	+ ${INSTALL_PROGRAM} gda.x $(BINDIR)/gda
159	+ ${INSTALL_PROGRAM} intedit.x $(BINDIR)/intedit
160	+ ${INSTALL_PROGRAM} intxyz.x $(BINDIR)/intxyz
161	+ ${INSTALL_PROGRAM} minimize.x $(BINDIR)/minimize
162	+ ${INSTALL_PROGRAM} minirot.x $(BINDIR)/minirot
163	+ ${INSTALL_PROGRAM} minrigid.x $(BINDIR)/minrigid
164	+ ${INSTALL_PROGRAM} monte.x $(BINDIR)/monte
165	+ ${INSTALL_PROGRAM} newton.x $(BINDIR)/newton
166	+ ${INSTALL_PROGRAM} newtrot.x $(BINDIR)/newtrot
167	+ ${INSTALL_PROGRAM} nucleic.x $(BINDIR)/nucleic
168	+ ${INSTALL_PROGRAM} optimize.x $(BINDIR)/optimize
169	+ ${INSTALL_PROGRAM} optirot.x $(BINDIR)/optirot
170	+ ${INSTALL_PROGRAM} optrigid.x $(BINDIR)/optrigid
171	+ ${INSTALL_PROGRAM} path.x $(BINDIR)/path
172	+ ${INSTALL_PROGRAM} pdbxyz.x $(BINDIR)/pdbxyz
173	+ ${INSTALL_PROGRAM} polarize.x $(BINDIR)/polarize
174	+ ${INSTALL_PROGRAM} poledit.x $(BINDIR)/poledit
175	+ ${INSTALL_PROGRAM} potential.x $(BINDIR)/potential
176	+ ${INSTALL_PROGRAM} prmedit.x $(BINDIR)/prmedit
177	+ ${INSTALL_PROGRAM} protein.x $(BINDIR)/protein
178	+ ${INSTALL_PROGRAM} pss.x $(BINDIR)/pss
179	+ ${INSTALL_PROGRAM} pssrigid.x $(BINDIR)/pssrigid
180	+ ${INSTALL_PROGRAM} pssrot.x $(BINDIR)/pssrot
181	+ ${INSTALL_PROGRAM} radial.x $(BINDIR)/radial
182	+ ${INSTALL_PROGRAM} saddle.x $(BINDIR)/saddle
183	+ ${INSTALL_PROGRAM} scan.x $(BINDIR)/scan
184	+ ${INSTALL_PROGRAM} sniffer.x $(BINDIR)/sniffer
185	+ ${INSTALL_PROGRAM} spacefill.x $(BINDIR)/spacefill
186	+ ${INSTALL_PROGRAM} spectrum.x $(BINDIR)/spectrum
187	+ ${INSTALL_PROGRAM} superpose.x $(BINDIR)/superpose
188	+ ${INSTALL_PROGRAM} sybylxyz.x $(BINDIR)/sybylxyz
189	+ ${INSTALL_PROGRAM} testgrad.x $(BINDIR)/testgrad
190	+ ${INSTALL_PROGRAM} testhess.x $(BINDIR)/testhess
191	+ ${INSTALL_PROGRAM} testpair.x $(BINDIR)/testpair
192	+ ${INSTALL_PROGRAM} testrot.x $(BINDIR)/testrot
193	+ ${INSTALL_PROGRAM} timer.x $(BINDIR)/timer
194	+ ${INSTALL_PROGRAM} timerot.x $(BINDIR)/timerot
195	+ ${INSTALL_PROGRAM} valence.x $(BINDIR)/valence
196	+ ${INSTALL_PROGRAM} vibbig.x $(BINDIR)/vibbig
197	+ ${INSTALL_PROGRAM} vibrate.x $(BINDIR)/vibrate
198	+ ${INSTALL_PROGRAM} vibrot.x $(BINDIR)/vibrot
199	+ ${INSTALL_PROGRAM} xtalfit.x $(BINDIR)/xtalfit
200	+ ${INSTALL_PROGRAM} xtalmin.x $(BINDIR)/xtalmin
201	+ ${INSTALL_PROGRAM} xyzedit.x $(BINDIR)/xyzedit
202	+ ${INSTALL_PROGRAM} xyzint.x $(BINDIR)/xyzint
203	+ ${INSTALL_PROGRAM} xyzpdb.x $(BINDIR)/xyzpdb
204	+ ${INSTALL_PROGRAM} xyzsybyl.x $(BINDIR)/xyzsybyl
205
206	remove_links:
207	rm -f $(LINKDIR)/alchemy

Line 0 Link Here

(-)biology/tinker/files/patch-make__Makefile (+209 lines)
		1	--- make/Makefile.orig 2011-11-06 05:29:19.000000000 +0900
		2	+++ make/Makefile 2011-11-23 05:37:09.000000000 +0900
		3	@@ -9,8 +9,8 @@
		4	##
		5	## 1. make all Build all the TINKER executables
		6	## 2. make rename Move the executables to BINDIR
		7	-## 3. make remove_links Create soft links in LINKDIR
		8	-## 4. make create_links Remove soft links from LINKDIR
		9	+## 3. make remove_links Remove soft links in LINKDIR
		10	+## 4. make create_links Create soft links from LINKDIR
		11	## 6. make listing Concatenate source to tinker.txt
		12	## 5. make clean Delete objects and executables
		13	##
		14	@@ -30,9 +30,9 @@
		15	## LINKDIR Linked Copies of TINKER Executables
		16	##
		17
		18	-TINKERDIR = /Users/ponder/tinker
		19	-BINDIR = $(TINKERDIR)/bin
		20	-LINKDIR = /usr/local/bin
		21	+TINKERDIR = ${WRKDIR}
		22	+BINDIR = ${PREFIX}/bin
		23	+#LINKDIR = /usr/local/bin
		24
		25	####################################################################
		26	## Known Machine Types; Uncomment One of the Following Sections ##
		27	@@ -40,6 +40,20 @@
		28	####################################################################
		29
		30	##
		31	+## Machine: IntelPC / FreeBSD
		32	+## CPU Type: Intel, AMD, Cyrix
		33	+## Oper Sys: FreeBSD 4.2
		34	+## Compiler: f77 , aka g77
		35	+##
		36	+
		37	+F77 = ${FC}
		38	+LIBS =
		39	+F77FLAGS = -c ${FFLAGS}
		40	+LINKFLAGS =
		41	+OPTFLAGS =
		42	+LIBFLAGS = -rcuv
		43	+
		44	+##
		45	## Machine: Generic Linux
		46	## CPU Type: Intel x86 Compatible
		47	## Oper Sys: Fedora Core
		48	@@ -104,12 +118,12 @@
		49	## Parallel: OpenMP
		50	##
		51
		52	-F77 = /opt/intel/bin/ifort
		53	-LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_threads -lfftw3
		54	-F77FLAGS = -c -axSSSE3 -assume cc_omp
		55	-OPTFLAGS = -O3 -no-ipo -no-prec-div -openmp
		56	-LIBFLAGS = -crusv
		57	-LINKFLAGS = $(OPTFLAGS) -static-intel -mmacosx-version-min=10.4
		58	+#F77 = /opt/intel/bin/ifort
		59	+#LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_threads -lfftw3
		60	+#F77FLAGS = -c -axSSSE3 -assume cc_omp
		61	+#OPTFLAGS = -O3 -no-ipo -no-prec-div -openmp
		62	+#LIBFLAGS = -crusv
		63	+#LINKFLAGS = $(OPTFLAGS) -static-intel -mmacosx-version-min=10.4
		64
65	##
66	## Machine: Macintosh
67	@@ -587,6 +601,8 @@
68	xyzpdb.x \
69	xyzsybyl.x
70
71	+.SUFFIXES: .x
72	+
73	.f.o:
74	${F77} ${F77FLAGS} ${OPTFLAGS} $*.f
75
76	@@ -596,8 +612,8 @@
77	server.o:
78	${F77} ${F77FLAGS} ${OPTFLAGS} server.f
79
80	-%.x: %.o libtinker.a
81	- ${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}; strip $@
82	+.o.x: libtinker.a
83	+ ${F77} ${LINKFLAGS} -o $@ $< libtinker.a ${LIBS}
84
85	all: ${EXEFILES}
86
87	@@ -608,64 +624,64 @@
88	cat .i .f *.c > tinker.txt
89
90	rename:
91	- mv alchemy.x $(BINDIR)/alchemy
92	- mv analyze.x $(BINDIR)/analyze
93	- mv anneal.x $(BINDIR)/anneal
94	- mv archive.x $(BINDIR)/archive
95	- mv correlate.x $(BINDIR)/correlate
96	- mv crystal.x $(BINDIR)/crystal
97	- mv diffuse.x $(BINDIR)/diffuse
98	- mv distgeom.x $(BINDIR)/distgeom
99	- mv document.x $(BINDIR)/document
100	- mv dynamic.x $(BINDIR)/dynamic
101	- mv gda.x $(BINDIR)/gda
102	- mv intedit.x $(BINDIR)/intedit
103	- mv intxyz.x $(BINDIR)/intxyz
104	- mv minimize.x $(BINDIR)/minimize
105	- mv minirot.x $(BINDIR)/minirot
106	- mv minrigid.x $(BINDIR)/minrigid
107	- mv monte.x $(BINDIR)/monte
108	- mv newton.x $(BINDIR)/newton
109	- mv newtrot.x $(BINDIR)/newtrot
110	- mv nucleic.x $(BINDIR)/nucleic
111	- mv optimize.x $(BINDIR)/optimize
112	- mv optirot.x $(BINDIR)/optirot
113	- mv optrigid.x $(BINDIR)/optrigid
114	- mv path.x $(BINDIR)/path
115	- mv pdbxyz.x $(BINDIR)/pdbxyz
116	- mv polarize.x $(BINDIR)/polarize
117	- mv poledit.x $(BINDIR)/poledit
118	- mv potential.x $(BINDIR)/potential
119	- mv prmedit.x $(BINDIR)/prmedit
120	- mv protein.x $(BINDIR)/protein
121	- mv pss.x $(BINDIR)/pss
122	- mv pssrigid.x $(BINDIR)/pssrigid
123	- mv pssrot.x $(BINDIR)/pssrot
124	- mv radial.x $(BINDIR)/radial
125	- mv saddle.x $(BINDIR)/saddle
126	- mv scan.x $(BINDIR)/scan
127	- mv sniffer.x $(BINDIR)/sniffer
128	- mv spacefill.x $(BINDIR)/spacefill
129	- mv spectrum.x $(BINDIR)/spectrum
130	- mv superpose.x $(BINDIR)/superpose
131	- mv sybylxyz.x $(BINDIR)/sybylxyz
132	- mv testgrad.x $(BINDIR)/testgrad
133	- mv testhess.x $(BINDIR)/testhess
134	- mv testpair.x $(BINDIR)/testpair
135	- mv testrot.x $(BINDIR)/testrot
136	- mv timer.x $(BINDIR)/timer
137	- mv timerot.x $(BINDIR)/timerot
138	- mv torsfit.x $(BINDIR)/torsfit
139	- mv valence.x $(BINDIR)/valence
140	- mv vibbig.x $(BINDIR)/vibbig
141	- mv vibrate.x $(BINDIR)/vibrate
142	- mv vibrot.x $(BINDIR)/vibrot
143	- mv xtalfit.x $(BINDIR)/xtalfit
144	- mv xtalmin.x $(BINDIR)/xtalmin
145	- mv xyzedit.x $(BINDIR)/xyzedit
146	- mv xyzint.x $(BINDIR)/xyzint
147	- mv xyzpdb.x $(BINDIR)/xyzpdb
148	- mv xyzsybyl.x $(BINDIR)/xyzsybyl
149	+ ${BSD_INSTALL_PROGRAM} alchemy.x $(BINDIR)/alchemy
150	+ ${BSD_INSTALL_PROGRAM} analyze.x $(BINDIR)/analyze
151	+ ${BSD_INSTALL_PROGRAM} anneal.x $(BINDIR)/anneal
152	+ ${BSD_INSTALL_PROGRAM} archive.x $(BINDIR)/archive
153	+ ${BSD_INSTALL_PROGRAM} correlate.x $(BINDIR)/correlate
154	+ ${BSD_INSTALL_PROGRAM} crystal.x $(BINDIR)/crystal
155	+ ${BSD_INSTALL_PROGRAM} diffuse.x $(BINDIR)/diffuse
156	+ ${BSD_INSTALL_PROGRAM} distgeom.x $(BINDIR)/distgeom
157	+ ${BSD_INSTALL_PROGRAM} document.x $(BINDIR)/document
158	+ ${BSD_INSTALL_PROGRAM} dynamic.x $(BINDIR)/dynamic
159	+ ${BSD_INSTALL_PROGRAM} gda.x $(BINDIR)/gda
160	+ ${BSD_INSTALL_PROGRAM} intedit.x $(BINDIR)/intedit
161	+ ${BSD_INSTALL_PROGRAM} intxyz.x $(BINDIR)/intxyz
162	+ ${BSD_INSTALL_PROGRAM} minimize.x $(BINDIR)/minimize
163	+ ${BSD_INSTALL_PROGRAM} minirot.x $(BINDIR)/minirot
164	+ ${BSD_INSTALL_PROGRAM} minrigid.x $(BINDIR)/minrigid
165	+ ${BSD_INSTALL_PROGRAM} monte.x $(BINDIR)/monte
166	+ ${BSD_INSTALL_PROGRAM} newton.x $(BINDIR)/newton
167	+ ${BSD_INSTALL_PROGRAM} newtrot.x $(BINDIR)/newtrot
168	+ ${BSD_INSTALL_PROGRAM} nucleic.x $(BINDIR)/nucleic
169	+ ${BSD_INSTALL_PROGRAM} optimize.x $(BINDIR)/optimize
170	+ ${BSD_INSTALL_PROGRAM} optirot.x $(BINDIR)/optirot
171	+ ${BSD_INSTALL_PROGRAM} optrigid.x $(BINDIR)/optrigid
172	+ ${BSD_INSTALL_PROGRAM} path.x $(BINDIR)/path
173	+ ${BSD_INSTALL_PROGRAM} pdbxyz.x $(BINDIR)/pdbxyz
174	+ ${BSD_INSTALL_PROGRAM} polarize.x $(BINDIR)/polarize
175	+ ${BSD_INSTALL_PROGRAM} poledit.x $(BINDIR)/poledit
176	+ ${BSD_INSTALL_PROGRAM} potential.x $(BINDIR)/potential
177	+ ${BSD_INSTALL_PROGRAM} prmedit.x $(BINDIR)/prmedit
178	+ ${BSD_INSTALL_PROGRAM} protein.x $(BINDIR)/protein
179	+ ${BSD_INSTALL_PROGRAM} pss.x $(BINDIR)/pss
180	+ ${BSD_INSTALL_PROGRAM} pssrigid.x $(BINDIR)/pssrigid
181	+ ${BSD_INSTALL_PROGRAM} pssrot.x $(BINDIR)/pssrot
182	+ ${BSD_INSTALL_PROGRAM} radial.x $(BINDIR)/radial
183	+ ${BSD_INSTALL_PROGRAM} saddle.x $(BINDIR)/saddle
184	+ ${BSD_INSTALL_PROGRAM} scan.x $(BINDIR)/scan
185	+ ${BSD_INSTALL_PROGRAM} sniffer.x $(BINDIR)/sniffer
186	+ ${BSD_INSTALL_PROGRAM} spacefill.x $(BINDIR)/spacefill
187	+ ${BSD_INSTALL_PROGRAM} spectrum.x $(BINDIR)/spectrum
188	+ ${BSD_INSTALL_PROGRAM} superpose.x $(BINDIR)/superpose
189	+ ${BSD_INSTALL_PROGRAM} sybylxyz.x $(BINDIR)/sybylxyz
190	+ ${BSD_INSTALL_PROGRAM} testgrad.x $(BINDIR)/testgrad
191	+ ${BSD_INSTALL_PROGRAM} testhess.x $(BINDIR)/testhess
192	+ ${BSD_INSTALL_PROGRAM} testpair.x $(BINDIR)/testpair
193	+ ${BSD_INSTALL_PROGRAM} testrot.x $(BINDIR)/testrot
194	+ ${BSD_INSTALL_PROGRAM} timer.x $(BINDIR)/timer
195	+ ${BSD_INSTALL_PROGRAM} timerot.x $(BINDIR)/timerot
196	+ ${BSD_INSTALL_PROGRAM} torsfit.x $(BINDIR)/torsfit
197	+ ${BSD_INSTALL_PROGRAM} valence.x $(BINDIR)/valence
198	+ ${BSD_INSTALL_PROGRAM} vibbig.x $(BINDIR)/vibbig
199	+ ${BSD_INSTALL_PROGRAM} vibrate.x $(BINDIR)/vibrate
200	+ ${BSD_INSTALL_PROGRAM} vibrot.x $(BINDIR)/vibrot
201	+ ${BSD_INSTALL_PROGRAM} xtalfit.x $(BINDIR)/xtalfit
202	+ ${BSD_INSTALL_PROGRAM} xtalmin.x $(BINDIR)/xtalmin
203	+ ${BSD_INSTALL_PROGRAM} xyzedit.x $(BINDIR)/xyzedit
204	+ ${BSD_INSTALL_PROGRAM} xyzint.x $(BINDIR)/xyzint
205	+ ${BSD_INSTALL_PROGRAM} xyzpdb.x $(BINDIR)/xyzpdb
206	+ ${BSD_INSTALL_PROGRAM} xyzsybyl.x $(BINDIR)/xyzsybyl
207
208	remove_links:
209	rm -f $(LINKDIR)/alchemy

Lines 45-50 Link Here

(-)biology/tinker/pkg-plist (-481 / +491 lines)
45	bin/testrot	45	bin/testrot
46	bin/timer	46	bin/timer
47	bin/timerot	47	bin/timerot
		48	bin/torsfit
48	bin/valence	49	bin/valence
49	bin/vibbig	50	bin/vibbig
50	bin/vibrate	51	bin/vibrate
Lines 61-481 Link Here
61	%%PORTDOCS%%%%DOCSDIR%%/guide.txt	62	%%PORTDOCS%%%%DOCSDIR%%/guide.txt
62	%%PORTDOCS%%%%DOCSDIR%%/license.pdf	63	%%PORTDOCS%%%%DOCSDIR%%/license.pdf
63	%%PORTDOCS%%%%DOCSDIR%%/license.txt	64	%%PORTDOCS%%%%DOCSDIR%%/license.txt
64	%%PORTDOCS%%%%DOCSDIR%%/release-3.2
65	%%PORTDOCS%%%%DOCSDIR%%/release-3.6
66	%%PORTDOCS%%%%DOCSDIR%%/release-3.7
67	%%PORTDOCS%%%%DOCSDIR%%/release-3.8
68	%%PORTDOCS%%%%DOCSDIR%%/release-3.9
69	%%PORTDOCS%%%%DOCSDIR%%/release-4.0
70	%%PORTDOCS%%%%DOCSDIR%%/release-4.1
71	%%PORTDOCS%%%%DOCSDIR%%/release-4.2
72	%%PORTDOCS%%%%DOCSDIR%%/summary.pdf	65	%%PORTDOCS%%%%DOCSDIR%%/summary.pdf
73	%%PORTDOCS%%%%DOCSDIR%%/summary.txt	66	%%PORTDOCS%%%%DOCSDIR%%/summary.txt
74	%%PORTDOCS%%%%EXAMPLESDIR%%/0README	67	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/0README
75	%%PORTDOCS%%%%EXAMPLESDIR%%/alatet.int	68	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alatet.int
76	%%PORTDOCS%%%%EXAMPLESDIR%%/alatet.key	69	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alatet.key
77	%%PORTDOCS%%%%EXAMPLESDIR%%/alatet.seq	70	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alatet.seq
78	%%PORTDOCS%%%%EXAMPLESDIR%%/alatet.xyz	71	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alatet.xyz
79	%%PORTDOCS%%%%EXAMPLESDIR%%/alkane.key	72	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alkane.key
80	%%PORTDOCS%%%%EXAMPLESDIR%%/alkane.xyz	73	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alkane.xyz
81	%%PORTDOCS%%%%EXAMPLESDIR%%/ammonia.key	74	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ammonia.key
82	%%PORTDOCS%%%%EXAMPLESDIR%%/ammonia.xyz	75	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ammonia.xyz
83	%%PORTDOCS%%%%EXAMPLESDIR%%/amoeba.key	76	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/amoeba.key
84	%%PORTDOCS%%%%EXAMPLESDIR%%/amoeba.xyz	77	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/amoeba.xyz
85	%%PORTDOCS%%%%EXAMPLESDIR%%/arach.int	78	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/arach.int
86	%%PORTDOCS%%%%EXAMPLESDIR%%/arach.key	79	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/arach.key
87	%%PORTDOCS%%%%EXAMPLESDIR%%/arach.xyz	80	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/arach.xyz
88	%%PORTDOCS%%%%EXAMPLESDIR%%/azulene.int	81	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/azulene.int
89	%%PORTDOCS%%%%EXAMPLESDIR%%/azulene.key	82	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/azulene.key
90	%%PORTDOCS%%%%EXAMPLESDIR%%/azulene.xyz	83	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/azulene.xyz