Index: head/science/tinker/Makefile =================================================================== --- head/science/tinker/Makefile (revision 554858) +++ head/science/tinker/Makefile (revision 554859) @@ -1,86 +1,86 @@ # Created by: Glenn Johnson # $FreeBSD$ PORTNAME= tinker -DISTVERSION= 8.8.1 +DISTVERSION= 8.8.3 CATEGORIES= science MASTER_SITES= https://dasher.wustl.edu/tinker/downloads/ MAINTAINER= yuri@FreeBSD.org COMMENT= General purpose molecular modelling package LICENSE= TINKER LICENSE_NAME= TINKER license agreement LICENSE_FILE= ${WRKSRC}/doc/license.pdf LICENSE_PERMS= auto-accept # internal academic purposes only, no commercial use LIB_DEPENDS= libfftw3.so:math/fftw3 USES= fortran gmake WRKSRC= ${WRKDIR}/${PORTNAME} BUILD_WRKSRC= ${WRKSRC}/source INSTALL_WRKSRC= ${WRKSRC}/source MAKE_ENV= HAVE_G2C=yes MAKE_ARGS= RANLIB=ranlib BINDIR=${STAGEDIR}${PREFIX}/bin MAKEFILE= ${WRKSRC}/make/Makefile EXTRACT_AFTER_ARGS=--exclude fftw --exclude windows --exclude macosx SUB_FILES= pkg-message BINARY_ALIAS= gfortran=gfortran${GCC_DEFAULT} OPTIONS_DEFINE= OPTIMIZED_FFLAGS DOCS EXAMPLES OPTIONS_DEFINE_amd64= SSE OPTIONS_DEFINE_i386= SSE OPTIONS_DEFAULT_amd64= SSE OPTIONS_DEFAULT_i386= SSE SSE_MAKE_ARGS= PORT_SIMD_FLAGS="-msse -msse2 -mfpmath=sse" OPTIMIZED_FFLAGS_DESC= compilation optimizations PORTDOCS= * PORTEXAMPLES= * .include .if ${PORT_OPTIONS:MOPTIMIZED_FFLAGS} FFLAGS+= -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations .if (${ARCH} == "i386") FFLAGS+= -mfancy-math-387 -malign-double .endif # i386 .endif post-extract: @${RM} ${BUILD_WRKSRC}/*.c @${RM} ${WRKSRC}/other/eopbend.orig post-patch: @${REINPLACE_CMD} -i '' 's|\.\./bin/|${STAGEDIR}${PREFIX}/bin/|' ${BUILD_WRKSRC}/../bench/bench*.run post-install: @${MKDIR} ${STAGEDIR}${DATADIR} @${MKDIR} ${STAGEDIR}${DATADIR}/params cd ${WRKSRC}/params && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR}/params @${MKDIR} ${STAGEDIR}${DATADIR}/test cd ${WRKSRC}/test && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR}/test post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} cd ${WRKSRC}/doc && ${INSTALL_DATA} 0README *.pdf ${STAGEDIR}${DOCSDIR} post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} cd ${WRKSRC}/example && ${INSTALL_DATA} \ 0README *.make *.dyn *.int *.frac *.key *.seq *.pdb *.xyz \ ${STAGEDIR}${EXAMPLESDIR} benchmarks: stage .for n in 1 2 3 4 5 6 7 8 9 @cd ${BUILD_WRKSRC}/../bench && ./bench${n}.run .endfor .include Index: head/science/tinker/distinfo =================================================================== --- head/science/tinker/distinfo (revision 554858) +++ head/science/tinker/distinfo (revision 554859) @@ -1,3 +1,3 @@ -TIMESTAMP = 1597694919 -SHA256 (tinker-8.8.1.tar.gz) = 8477afb51a0dcbba421948645eb77df3d071de984440b2e2d14063f9477e6d2e -SIZE (tinker-8.8.1.tar.gz) = 69052620 +TIMESTAMP = 1605046844 +SHA256 (tinker-8.8.3.tar.gz) = 9f874ffc8d3b996e0b44ee1ee58759de0352e11767155a9dd80d63979e5957d4 +SIZE (tinker-8.8.3.tar.gz) = 69516061 Index: head/science/tinker/files/patch-make_Makefile =================================================================== --- head/science/tinker/files/patch-make_Makefile (revision 554858) +++ head/science/tinker/files/patch-make_Makefile (revision 554859) @@ -1,271 +1,275 @@ ---- make/Makefile.orig 2020-07-27 02:52:19 UTC +--- make/Makefile.orig 2020-11-09 22:09:06 UTC +++ make/Makefile @@ -87,9 +87,9 @@ APBS_LIBS = -lapbsmainroutines -lapbs -lmaloc -lapbsbl F77 = gfortran F77FLAGS = -c #OPTFLAGS = -Ofast -march=native -fopenmp -OPTFLAGS = -Ofast -mssse3 -fopenmp +OPTFLAGS = -Ofast $(PORT_SIMD_FLAGS) -fopenmp #OPTFLAGS = -Og -fbacktrace -fcheck=bounds -Wunused -Wmaybe-uninitialized -LIBDIR = -L. -L$(TINKER_LIBDIR)/macos +#LIBDIR = -L. -L$(TINKER_LIBDIR)/macos LIBS = LIBFLAGS = -crusv RANLIB = ranlib -c -@@ -813,132 +813,132 @@ listing: +@@ -817,134 +817,134 @@ listing: cat *.f *.c > tinker.txt rename_bin: - mv alchemy.x $(BINDIR)/alchemy - mv analyze.x $(BINDIR)/analyze - mv anneal.x $(BINDIR)/anneal - mv archive.x $(BINDIR)/archive - mv bar.x $(BINDIR)/bar - mv correlate.x $(BINDIR)/correlate +- mv critical.x $(BINDIR)/critical - 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 mol2xyz.x $(BINDIR)/mol2xyz - mv molxyz.x $(BINDIR)/molxyz - 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 testgrad.x $(BINDIR)/testgrad - mv testhess.x $(BINDIR)/testhess - mv testpair.x $(BINDIR)/testpair - mv testpol.x $(BINDIR)/testpol - mv testrot.x $(BINDIR)/testrot - mv testvir.x $(BINDIR)/testvir - 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 xyzmol2.x $(BINDIR)/xyzmol2 - mv xyzpdb.x $(BINDIR)/xyzpdb + ${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} bar.x $(BINDIR)/bar + ${BSD_INSTALL_PROGRAM} correlate.x $(BINDIR)/correlate ++ ${BSD_INSTALL_PROGRAM} critical.x $(BINDIR)/critical + ${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} mol2xyz.x $(BINDIR)/mol2xyz + ${BSD_INSTALL_PROGRAM} molxyz.x $(BINDIR)/molxyz + ${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} testgrad.x $(BINDIR)/testgrad + ${BSD_INSTALL_PROGRAM} testhess.x $(BINDIR)/testhess + ${BSD_INSTALL_PROGRAM} testpair.x $(BINDIR)/testpair + ${BSD_INSTALL_PROGRAM} testpol.x $(BINDIR)/testpol + ${BSD_INSTALL_PROGRAM} testrot.x $(BINDIR)/testrot + ${BSD_INSTALL_PROGRAM} testvir.x $(BINDIR)/testvir + ${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} xyzmol2.x $(BINDIR)/xyzmol2 + ${BSD_INSTALL_PROGRAM} xyzpdb.x $(BINDIR)/xyzpdb rename_exe: - mv alchemy.x $(BINDIR)/alchemy.exe - mv analyze.x $(BINDIR)/analyze.exe - mv anneal.x $(BINDIR)/anneal.exe - mv archive.x $(BINDIR)/archive.exe - mv bar.x $(BINDIR)/bar.exe - mv correlate.x $(BINDIR)/correlate.exe +- mv critical.x $(BINDIR)/critical.exe - mv crystal.x $(BINDIR)/crystal.exe - mv diffuse.x $(BINDIR)/diffuse.exe - mv distgeom.x $(BINDIR)/distgeom.exe - mv document.x $(BINDIR)/document.exe - mv dynamic.x $(BINDIR)/dynamic.exe - mv gda.x $(BINDIR)/gda.exe - mv intedit.x $(BINDIR)/intedit.exe - mv intxyz.x $(BINDIR)/intxyz.exe - mv minimize.x $(BINDIR)/minimize.exe - mv minirot.x $(BINDIR)/minirot.exe - mv minrigid.x $(BINDIR)/minrigid.exe - mv mol2xyz.x $(BINDIR)/mol2xyz.exe - mv molxyz.x $(BINDIR)/molxyz.exe - mv monte.x $(BINDIR)/monte.exe - mv newton.x $(BINDIR)/newton.exe - mv newtrot.x $(BINDIR)/newtrot.exe - mv nucleic.x $(BINDIR)/nucleic.exe - mv optimize.x $(BINDIR)/optimize.exe - mv optirot.x $(BINDIR)/optirot.exe - mv optrigid.x $(BINDIR)/optrigid.exe - mv path.x $(BINDIR)/path.exe - mv pdbxyz.x $(BINDIR)/pdbxyz.exe - mv polarize.x $(BINDIR)/polarize.exe - mv poledit.x $(BINDIR)/poledit.exe - mv potential.x $(BINDIR)/potential.exe - mv prmedit.x $(BINDIR)/prmedit.exe - mv protein.x $(BINDIR)/protein.exe - mv pss.x $(BINDIR)/pss.exe - mv pssrigid.x $(BINDIR)/pssrigid.exe - mv pssrot.x $(BINDIR)/pssrot.exe - mv radial.x $(BINDIR)/radial.exe - mv saddle.x $(BINDIR)/saddle.exe - mv scan.x $(BINDIR)/scan.exe - mv sniffer.x $(BINDIR)/sniffer.exe - mv spacefill.x $(BINDIR)/spacefill.exe - mv spectrum.x $(BINDIR)/spectrum.exe - mv superpose.x $(BINDIR)/superpose.exe - mv testgrad.x $(BINDIR)/testgrad.exe - mv testhess.x $(BINDIR)/testhess.exe - mv testpair.x $(BINDIR)/testpair.exe - mv testpol.x $(BINDIR)/testpol.exe - mv testrot.x $(BINDIR)/testrot.exe - mv testvir.x $(BINDIR)/testvir.exe - mv timer.x $(BINDIR)/timer.exe - mv timerot.x $(BINDIR)/timerot.exe - mv torsfit.x $(BINDIR)/torsfit.exe - mv valence.x $(BINDIR)/valence.exe - mv vibbig.x $(BINDIR)/vibbig.exe - mv vibrate.x $(BINDIR)/vibrate.exe - mv vibrot.x $(BINDIR)/vibrot.exe - mv xtalfit.x $(BINDIR)/xtalfit.exe - mv xtalmin.x $(BINDIR)/xtalmin.exe - mv xyzedit.x $(BINDIR)/xyzedit.exe - mv xyzint.x $(BINDIR)/xyzint.exe - mv xyzmol2.x $(BINDIR)/xyzmol2.exe - mv xyzpdb.x $(BINDIR)/xyzpdb.exe + ${BSD_INSTALL_PROGRAM} alchemy.x $(BINDIR)/alchemy.exe + ${BSD_INSTALL_PROGRAM} analyze.x $(BINDIR)/analyze.exe + ${BSD_INSTALL_PROGRAM} anneal.x $(BINDIR)/anneal.exe + ${BSD_INSTALL_PROGRAM} archive.x $(BINDIR)/archive.exe + ${BSD_INSTALL_PROGRAM} bar.x $(BINDIR)/bar.exe + ${BSD_INSTALL_PROGRAM} correlate.x $(BINDIR)/correlate.exe ++ ${BSD_INSTALL_PROGRAM} critical.x $(BINDIR)/critical.exe + ${BSD_INSTALL_PROGRAM} crystal.x $(BINDIR)/crystal.exe + ${BSD_INSTALL_PROGRAM} diffuse.x $(BINDIR)/diffuse.exe + ${BSD_INSTALL_PROGRAM} distgeom.x $(BINDIR)/distgeom.exe + ${BSD_INSTALL_PROGRAM} document.x $(BINDIR)/document.exe + ${BSD_INSTALL_PROGRAM} dynamic.x $(BINDIR)/dynamic.exe + ${BSD_INSTALL_PROGRAM} gda.x $(BINDIR)/gda.exe + ${BSD_INSTALL_PROGRAM} intedit.x $(BINDIR)/intedit.exe + ${BSD_INSTALL_PROGRAM} intxyz.x $(BINDIR)/intxyz.exe + ${BSD_INSTALL_PROGRAM} minimize.x $(BINDIR)/minimize.exe + ${BSD_INSTALL_PROGRAM} minirot.x $(BINDIR)/minirot.exe + ${BSD_INSTALL_PROGRAM} minrigid.x $(BINDIR)/minrigid.exe + ${BSD_INSTALL_PROGRAM} mol2xyz.x $(BINDIR)/mol2xyz.exe + ${BSD_INSTALL_PROGRAM} molxyz.x $(BINDIR)/molxyz.exe + ${BSD_INSTALL_PROGRAM} monte.x $(BINDIR)/monte.exe + ${BSD_INSTALL_PROGRAM} newton.x $(BINDIR)/newton.exe + ${BSD_INSTALL_PROGRAM} newtrot.x $(BINDIR)/newtrot.exe + ${BSD_INSTALL_PROGRAM} nucleic.x $(BINDIR)/nucleic.exe + ${BSD_INSTALL_PROGRAM} optimize.x $(BINDIR)/optimize.exe + ${BSD_INSTALL_PROGRAM} optirot.x $(BINDIR)/optirot.exe + ${BSD_INSTALL_PROGRAM} optrigid.x $(BINDIR)/optrigid.exe + ${BSD_INSTALL_PROGRAM} path.x $(BINDIR)/path.exe + ${BSD_INSTALL_PROGRAM} pdbxyz.x $(BINDIR)/pdbxyz.exe + ${BSD_INSTALL_PROGRAM} polarize.x $(BINDIR)/polarize.exe + ${BSD_INSTALL_PROGRAM} poledit.x $(BINDIR)/poledit.exe + ${BSD_INSTALL_PROGRAM} potential.x $(BINDIR)/potential.exe + ${BSD_INSTALL_PROGRAM} prmedit.x $(BINDIR)/prmedit.exe + ${BSD_INSTALL_PROGRAM} protein.x $(BINDIR)/protein.exe + ${BSD_INSTALL_PROGRAM} pss.x $(BINDIR)/pss.exe + ${BSD_INSTALL_PROGRAM} pssrigid.x $(BINDIR)/pssrigid.exe + ${BSD_INSTALL_PROGRAM} pssrot.x $(BINDIR)/pssrot.exe + ${BSD_INSTALL_PROGRAM} radial.x $(BINDIR)/radial.exe + ${BSD_INSTALL_PROGRAM} saddle.x $(BINDIR)/saddle.exe + ${BSD_INSTALL_PROGRAM} scan.x $(BINDIR)/scan.exe + ${BSD_INSTALL_PROGRAM} sniffer.x $(BINDIR)/sniffer.exe + ${BSD_INSTALL_PROGRAM} spacefill.x $(BINDIR)/spacefill.exe + ${BSD_INSTALL_PROGRAM} spectrum.x $(BINDIR)/spectrum.exe + ${BSD_INSTALL_PROGRAM} superpose.x $(BINDIR)/superpose.exe + ${BSD_INSTALL_PROGRAM} testgrad.x $(BINDIR)/testgrad.exe + ${BSD_INSTALL_PROGRAM} testhess.x $(BINDIR)/testhess.exe + ${BSD_INSTALL_PROGRAM} testpair.x $(BINDIR)/testpair.exe + ${BSD_INSTALL_PROGRAM} testpol.x $(BINDIR)/testpol.exe + ${BSD_INSTALL_PROGRAM} testrot.x $(BINDIR)/testrot.exe + ${BSD_INSTALL_PROGRAM} testvir.x $(BINDIR)/testvir.exe + ${BSD_INSTALL_PROGRAM} timer.x $(BINDIR)/timer.exe + ${BSD_INSTALL_PROGRAM} timerot.x $(BINDIR)/timerot.exe + ${BSD_INSTALL_PROGRAM} torsfit.x $(BINDIR)/torsfit.exe + ${BSD_INSTALL_PROGRAM} valence.x $(BINDIR)/valence.exe + ${BSD_INSTALL_PROGRAM} vibbig.x $(BINDIR)/vibbig.exe + ${BSD_INSTALL_PROGRAM} vibrate.x $(BINDIR)/vibrate.exe + ${BSD_INSTALL_PROGRAM} vibrot.x $(BINDIR)/vibrot.exe + ${BSD_INSTALL_PROGRAM} xtalfit.x $(BINDIR)/xtalfit.exe + ${BSD_INSTALL_PROGRAM} xtalmin.x $(BINDIR)/xtalmin.exe + ${BSD_INSTALL_PROGRAM} xyzedit.x $(BINDIR)/xyzedit.exe + ${BSD_INSTALL_PROGRAM} xyzint.x $(BINDIR)/xyzint.exe + ${BSD_INSTALL_PROGRAM} xyzmol2.x $(BINDIR)/xyzmol2.exe + ${BSD_INSTALL_PROGRAM} xyzpdb.x $(BINDIR)/xyzpdb.exe remove_links: rm -f $(LINKDIR)/alchemy Index: head/science/tinker/pkg-plist =================================================================== --- head/science/tinker/pkg-plist (revision 554858) +++ head/science/tinker/pkg-plist (revision 554859) @@ -1,196 +1,199 @@ bin/alchemy bin/analyze bin/anneal bin/archive bin/bar bin/correlate +bin/critical bin/crystal bin/diffuse bin/distgeom bin/document bin/dynamic bin/gda bin/intedit bin/intxyz bin/minimize bin/minirot bin/minrigid bin/mol2xyz bin/molxyz bin/monte bin/newton bin/newtrot bin/nucleic bin/optimize bin/optirot bin/optrigid bin/path bin/pdbxyz bin/polarize bin/poledit bin/potential bin/prmedit bin/protein bin/pss bin/pssrigid bin/pssrot bin/radial bin/saddle bin/scan bin/sniffer bin/spacefill bin/spectrum bin/superpose bin/testgrad bin/testhess bin/testpair bin/testpol bin/testrot bin/testvir bin/timer bin/timerot bin/torsfit bin/valence bin/vibbig bin/vibrate bin/vibrot bin/xtalfit bin/xtalmin bin/xyzedit bin/xyzint bin/xyzmol2 bin/xyzpdb %%DATADIR%%/params/0README %%DATADIR%%/params/amber94.prm %%DATADIR%%/params/amber96.prm %%DATADIR%%/params/amber98.prm %%DATADIR%%/params/amber99.prm %%DATADIR%%/params/amber99sb.prm %%DATADIR%%/params/amoeba04.prm %%DATADIR%%/params/amoeba09.prm %%DATADIR%%/params/amoebabio09.prm %%DATADIR%%/params/amoebabio18.prm %%DATADIR%%/params/amoebanuc17.prm %%DATADIR%%/params/amoebaplus.prm %%DATADIR%%/params/amoebapluscf.prm %%DATADIR%%/params/amoebapro04.prm %%DATADIR%%/params/amoebapro13.prm %%DATADIR%%/params/charmm19.prm %%DATADIR%%/params/charmm22.prm %%DATADIR%%/params/charmm22cmap.prm %%DATADIR%%/params/dang.prm %%DATADIR%%/params/hippo19.prm %%DATADIR%%/params/hoch.prm %%DATADIR%%/params/iwater.prm %%DATADIR%%/params/mm2.prm %%DATADIR%%/params/mm3.prm %%DATADIR%%/params/mm3pro.prm %%DATADIR%%/params/mmff.prm %%DATADIR%%/params/oplsaa.prm %%DATADIR%%/params/oplsaal.prm %%DATADIR%%/params/oplsua.prm %%DATADIR%%/params/smoothaa.prm %%DATADIR%%/params/smoothua.prm %%DATADIR%%/params/tiny.prm +%%DATADIR%%/params/uwater.prm %%DATADIR%%/params/water03.prm %%DATADIR%%/params/water14.prm %%DATADIR%%/params/water19.prm %%DATADIR%%/test/0README %%DATADIR%%/test/anion.dat %%DATADIR%%/test/anion.dyn0 %%DATADIR%%/test/anion.key %%DATADIR%%/test/anion.log %%DATADIR%%/test/anion.run %%DATADIR%%/test/anion.xyz %%DATADIR%%/test/argon.1st %%DATADIR%%/test/argon.key %%DATADIR%%/test/argon.log %%DATADIR%%/test/argon.run %%DATADIR%%/test/cluster.dat %%DATADIR%%/test/cluster.key %%DATADIR%%/test/cluster.log %%DATADIR%%/test/cluster.run %%DATADIR%%/test/cluster.xyz %%DATADIR%%/test/crambin.key %%DATADIR%%/test/crambin.log %%DATADIR%%/test/crambin.pdb %%DATADIR%%/test/crambin.run %%DATADIR%%/test/cyclohex.boat %%DATADIR%%/test/cyclohex.chair %%DATADIR%%/test/cyclohex.key %%DATADIR%%/test/cyclohex.log %%DATADIR%%/test/cyclohex.run %%DATADIR%%/test/dhfr.dyn %%DATADIR%%/test/dhfr.key %%DATADIR%%/test/dhfr.log %%DATADIR%%/test/dhfr.run %%DATADIR%%/test/dhfr.xyz %%DATADIR%%/test/dialanine.key %%DATADIR%%/test/dialanine.log %%DATADIR%%/test/dialanine.run %%DATADIR%%/test/dialanine.xyz %%DATADIR%%/test/enkephalin.dat %%DATADIR%%/test/enkephalin.key %%DATADIR%%/test/enkephalin.log %%DATADIR%%/test/enkephalin.run %%DATADIR%%/test/ethanol.000 %%DATADIR%%/test/ethanol.020 %%DATADIR%%/test/ethanol.040 %%DATADIR%%/test/ethanol.060 %%DATADIR%%/test/ethanol.080 %%DATADIR%%/test/ethanol.100 %%DATADIR%%/test/ethanol.120 %%DATADIR%%/test/ethanol.140 %%DATADIR%%/test/ethanol.160 %%DATADIR%%/test/ethanol.180 %%DATADIR%%/test/ethanol.dat %%DATADIR%%/test/ethanol.key %%DATADIR%%/test/ethanol.log %%DATADIR%%/test/ethanol.run %%DATADIR%%/test/ethanol.xyz %%DATADIR%%/test/formamide.cell %%DATADIR%%/test/formamide.dat %%DATADIR%%/test/formamide.key %%DATADIR%%/test/formamide.log %%DATADIR%%/test/formamide.run %%DATADIR%%/test/gpcr.blk %%DATADIR%%/test/gpcr.key %%DATADIR%%/test/gpcr.log +%%DATADIR%%/test/gpcr.old %%DATADIR%%/test/gpcr.run %%DATADIR%%/test/gpcr.xyz %%DATADIR%%/test/helix.1st %%DATADIR%%/test/helix.key %%DATADIR%%/test/helix.log %%DATADIR%%/test/helix.run %%DATADIR%%/test/ice.key %%DATADIR%%/test/ice.log %%DATADIR%%/test/ice.run %%DATADIR%%/test/ice.xyz %%DATADIR%%/test/ifabp.dat %%DATADIR%%/test/ifabp.key %%DATADIR%%/test/ifabp.log %%DATADIR%%/test/ifabp.run %%DATADIR%%/test/ifabp.xyz %%DATADIR%%/test/methanol.dat %%DATADIR%%/test/methanol.dma %%DATADIR%%/test/methanol.key %%DATADIR%%/test/methanol.log %%DATADIR%%/test/methanol.run %%DATADIR%%/test/nitrogen.arc %%DATADIR%%/test/nitrogen.key %%DATADIR%%/test/nitrogen.log %%DATADIR%%/test/nitrogen.run %%DATADIR%%/test/nitrogen.xyz %%DATADIR%%/test/salt.cell %%DATADIR%%/test/salt.key %%DATADIR%%/test/salt.log %%DATADIR%%/test/salt.run %%DATADIR%%/test/tetraala.dat %%DATADIR%%/test/tetraala.key %%DATADIR%%/test/tetraala.log %%DATADIR%%/test/tetraala.run %%DATADIR%%/test/water.key %%DATADIR%%/test/water.log %%DATADIR%%/test/water.pot %%DATADIR%%/test/water.run %%DATADIR%%/test/water.xyz