diff --git a/science/tinker/Makefile b/science/tinker/Makefile index 3a5cb18b0c75..f66cb43850b0 100644 --- a/science/tinker/Makefile +++ b/science/tinker/Makefile @@ -1,97 +1,97 @@ PORTNAME= tinker DISTVERSIONPREFIX= v -DISTVERSION= 25.5.2 +DISTVERSION= 25.5.4 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= General purpose molecular modelling package WWW= https://dasher.wustl.edu/tinker/ \ https://github.com/TinkerTools/tinker 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 USE_GITHUB= yes GH_ACCOUNT= TinkerTools BUILD_WRKSRC= ${WRKSRC}/source INSTALL_WRKSRC= ${WRKSRC}/source MAKE_ENV= HAVE_G2C=yes MAKE_ARGS= RANLIB=ranlib BINDIR=${STAGEDIR}${PREFIX}/bin LIBS="${LOCALBASE}/lib/libfftw3.a ${LOCALBASE}/lib/libfftw3_threads.a" 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= NATIVE OPTIMIZED_FFLAGS DOCS EXAMPLES OPTIONS_DEFINE_amd64= SIMD OPTIONS_DEFINE_i386= SIMD NATIVE_MAKE_ARGS= PORT_SIMD_FLAGS+="-march=native" OPTIMIZED_FFLAGS_DESC= Fortran compilation optimizations SIMD_MAKE_ARGS= PORT_SIMD_FLAGS+="-msse -msse2 -mssse3" 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 # OPTIMIZED_FFLAGS post-extract: @${RM} ${BUILD_WRKSRC}/*.c @${RM} ${WRKSRC}/other/eopbend.orig # remove bundled linux libraries @${RM} ${WRKSRC}/lib/linux/* post-patch: @${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} do-test: ${RM} -r ${WRKSRC}/bin ${LN} -s ${STAGEDIR}${PREFIX}/bin ${WRKSRC}/bin cd ${WRKSRC}/test && \ for test_run in *.run; do \ ${ECHO} "Running test $${test_run} ..." && \ ./$${test_run} && \ ${ECHO} "Test $${test_run} suceeded"; \ done benchmarks: stage .for n in 1 2 3 4 5 6 7 8 9 @cd ${BUILD_WRKSRC}/../bench && ./bench${n}.run .endfor .include diff --git a/science/tinker/distinfo b/science/tinker/distinfo index da2498d5f92a..c80318510948 100644 --- a/science/tinker/distinfo +++ b/science/tinker/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1760108472 -SHA256 (TinkerTools-tinker-v25.5.2_GH0.tar.gz) = 3a474a892892ab0b77a86599dd57c17731c64c363af7e48cfe6915a6d4276df6 -SIZE (TinkerTools-tinker-v25.5.2_GH0.tar.gz) = 34670489 +TIMESTAMP = 1763921430 +SHA256 (TinkerTools-tinker-v25.5.4_GH0.tar.gz) = 410d02d3fe7b42b124cc38cef8cf3c077037a099465c799259f60bdae4e367b2 +SIZE (TinkerTools-tinker-v25.5.4_GH0.tar.gz) = 34197683 diff --git a/science/tinker/files/patch-make_Makefile b/science/tinker/files/patch-make_Makefile index 7e1f679a86a0..b92cb6e976c7 100644 --- a/science/tinker/files/patch-make_Makefile +++ b/science/tinker/files/patch-make_Makefile @@ -1,271 +1,141 @@ ---- make/Makefile.orig 2025-09-30 16:25:57 UTC +--- make/Makefile.orig 2025-11-21 04:02:18 UTC +++ make/Makefile -@@ -813,138 +813,138 @@ rename_bin: +@@ -818,72 +818,72 @@ rename_bin: cat *.f *.c > tinker.txt rename_bin: - mv alchemy.x $(BINDIR)/alchemy - mv analyze.x $(BINDIR)/analyze - mv anneal.x $(BINDIR)/anneal - mv arcedit.x $(BINDIR)/arcedit - 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 freefix.x $(BINDIR)/freefix - mv gda.x $(BINDIR)/gda - mv intedit.x $(BINDIR)/intedit - mv intxyz.x $(BINDIR)/intxyz +- mv mdavg.x $(BINDIR)/mdavg - 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 testsurf.x $(BINDIR)/testsurf - 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} arcedit.x $(BINDIR)/arcedit + ${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} freefix.x $(BINDIR)/freefix + ${BSD_INSTALL_PROGRAM} gda.x $(BINDIR)/gda + ${BSD_INSTALL_PROGRAM} intedit.x $(BINDIR)/intedit + ${BSD_INSTALL_PROGRAM} intxyz.x $(BINDIR)/intxyz ++ ${BSD_INSTALL_PROGRAM} mdavg.x $(BINDIR)/mdavg + ${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} testsurf.x $(BINDIR)/testsurf + ${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 arcedit.x $(BINDIR)/arcedit.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 freefix.x $(BINDIR)/freefix.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 testsurf.x $(BINDIR)/testsurf.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} arcedit.x $(BINDIR)/arcedit.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} freefix.x $(BINDIR)/freefix.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} testsurf.x $(BINDIR)/testsurf.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 + mv alchemy.x $(BINDIR)/alchemy.exe diff --git a/science/tinker/pkg-plist b/science/tinker/pkg-plist index b0f9367ade44..cf05ef8ea37c 100644 --- a/science/tinker/pkg-plist +++ b/science/tinker/pkg-plist @@ -1,231 +1,232 @@ bin/alchemy bin/analyze bin/anneal bin/arcedit bin/bar bin/correlate bin/critical bin/crystal bin/diffuse bin/distgeom bin/document bin/dynamic bin/freefix bin/gda bin/intedit bin/intxyz +bin/mdavg 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/testsurf 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/amber14sb.prm %%DATADIR%%/params/amber19sb.prm %%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/amoebabio-hfc23.prm %%DATADIR%%/params/amoebabio09.prm %%DATADIR%%/params/amoebabio18.prm %%DATADIR%%/params/amoebail22.prm %%DATADIR%%/params/amoebanuc17.prm %%DATADIR%%/params/amoebaplus.prm %%DATADIR%%/params/amoebapro04.prm %%DATADIR%%/params/amoebapro13.prm %%DATADIR%%/params/basic.prm %%DATADIR%%/params/charmm19.prm %%DATADIR%%/params/charmm22.prm %%DATADIR%%/params/charmm27.prm -%%DATADIR%%/params/charmm36.prm +%%DATADIR%%/params/charmm36m.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/mmff94.prm %%DATADIR%%/params/mmff94s.prm %%DATADIR%%/params/oplsaa08.prm %%DATADIR%%/params/oplsaal.prm %%DATADIR%%/params/oplsua.prm %%DATADIR%%/params/smoothaa.prm %%DATADIR%%/params/smoothua.prm %%DATADIR%%/params/uwater.prm %%DATADIR%%/params/water03.prm %%DATADIR%%/params/water14.prm %%DATADIR%%/params/water21.prm %%DATADIR%%/params/water22.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/cation.ckey %%DATADIR%%/test/cation.cxyz %%DATADIR%%/test/cation.log %%DATADIR%%/test/cation.rkey %%DATADIR%%/test/cation.run %%DATADIR%%/test/cation.rxyz %%DATADIR%%/test/clean.make %%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/cyclohexane.boat %%DATADIR%%/test/cyclohexane.chair %%DATADIR%%/test/cyclohexane.key %%DATADIR%%/test/cyclohexane.log %%DATADIR%%/test/cyclohexane.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 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