From 84a792753de77f1ad3c84895d54491cd3f2104de Mon Sep 17 00:00:00 2001 From: ehaupt Date: Fri, 5 May 2006 20:09:54 +0000 Subject: Add protomol 2.0.3, OO, component based, framework for molecular dynamics (MD) simulations. PR: 95123 Submitted by: Sangwoo Shim --- biology/Makefile | 1 + biology/protomol/Makefile | 54 +++++++++++++++++++ biology/protomol/distinfo | 3 ++ biology/protomol/pkg-descr | 15 ++++++ biology/protomol/pkg-plist | 128 +++++++++++++++++++++++++++++++++++++++++++++ 5 files changed, 201 insertions(+) create mode 100644 biology/protomol/Makefile create mode 100644 biology/protomol/distinfo create mode 100644 biology/protomol/pkg-descr create mode 100644 biology/protomol/pkg-plist diff --git a/biology/Makefile b/biology/Makefile index 294332a06eef..4e3db307679d 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -57,6 +57,7 @@ SUBDIR += platon SUBDIR += povchem SUBDIR += primer3 + SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-biopython SUBDIR += pymol diff --git a/biology/protomol/Makefile b/biology/protomol/Makefile new file mode 100644 index 000000000000..39252c9bd9f7 --- /dev/null +++ b/biology/protomol/Makefile @@ -0,0 +1,54 @@ +# New ports collection makefile for: protomol +# Date created: 5 May 2006 +# Whom: Sangwoo Shim +# +# $FreeBSD$ + +PORTNAME= protomol +PORTVERSION= 2.0.3 +CATEGORIES= biology +MASTER_SITES= ${MASTER_SITE_SOURCEFORGE} +MASTER_SITE_SUBDIR= ${PORTNAME} +DISTNAME= ${PORTNAME}-${PORTVERSION}-tar.gz +EXTRACT_SUFX= # nada + +MAINTAINER= sangwoos@gmail.com +COMMENT= OO, component based, framework for molecular dynamics (MD) simulations + +LIB_DEPENDS= png.5:${PORTSDIR}/graphics/png \ + jpeg.9:${PORTSDIR}/graphics/jpeg \ + tiff.4:${PORTSDIR}/graphics/tiff + +GNU_CONFIGURE= yes +USE_XLIB= yes +USE_GCC= 3.4+ + +# Hack to cure a misbehavior of the configure script +CONFIGURE_ARGS+= --without-irix_mipspro_mpi + +CPPFLAGS+= -I${LOCALBASE}/include -I${X11BASE}/include +CXXFLAGS+= -L${LOCALBASE}/lib -L${X11BASE}/lib + +CONFIGURE_ENV+= CPPFLAGS="${CPPFLAGS}" CXXFLAGS="${CXXFLAGS}" + +WRKSRC= ${WRKDIR}/${PORTNAME} + +OPTIONS= GLUT "Use glut" on + +.include + +.if defined(WITH_GLUT) +CONFIGURE_ARGS+= --with-glut=yes +LIB_DEPENDS+= glut.4:${PORTSDIR}/graphics/libglut +.else +CONFIGURE_ARGS+= --with-glut=no +.endif + +.if !defined(NOPORTDOCS) +post-install: + @${MKDIR} ${EXAMPLESDIR} + cd ${WRKSRC}/examples && ${FIND} . | ${EGREP} -v '\.cvsignore' | \ + ${CPIO} -pdmu -R ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR} +.endif + +.include diff --git a/biology/protomol/distinfo b/biology/protomol/distinfo new file mode 100644 index 000000000000..e38c28376e65 --- /dev/null +++ b/biology/protomol/distinfo @@ -0,0 +1,3 @@ +MD5 (protomol-2.0.3-tar.gz) = 0c0f1749c7dd88c280e9b2563e853a68 +SHA256 (protomol-2.0.3-tar.gz) = 52c5faf69c717516a2b071dabbaed089ae7e9944b706e391e74604946a69c183 +SIZE (protomol-2.0.3-tar.gz) = 2391568 diff --git a/biology/protomol/pkg-descr b/biology/protomol/pkg-descr new file mode 100644 index 000000000000..8a0b7239b89d --- /dev/null +++ b/biology/protomol/pkg-descr @@ -0,0 +1,15 @@ +ProtoMol is an object-oriented, component based, framework for molecular +dynamics (MD) simulations. The framework supports the CHARMM 19 and 28a2 force +fields and is able to process PDB, PSF, XYZ and DCD trajectory files. It is +designed for high flexibility, easy extendibility and maintenance, and high +performance demands, including parallelization. The technique of multiple +time-stepping is used to improve long-term efficiency. The use of fast +electrostatic force evaluation algorithms like Ewald, particle Mesh Ewald (PME), +and Multigrid (MG) summation further enhances performance. Longer time steps +are possible using MOLLY, Langevin Molly and Hybrid Monte Carlo, Nose-Hoover, +and Langevin integrators. In addition, ProtoMol has been designed to interact +with VMD, a visualization engine developed by the University of Illinois that is +used for displaying large biomolecular systems in three dimensions. ProtoMol is +freely distributed software, and the source code is available. + +WWW: http://protomol.sourceforge.net/ diff --git a/biology/protomol/pkg-plist b/biology/protomol/pkg-plist new file mode 100644 index 000000000000..1823d8daeb80 --- /dev/null +++ b/biology/protomol/pkg-plist @@ -0,0 +1,128 @@ +bin/coords2coords +bin/coulomb +bin/dcd2dcd +bin/iSGProtomol +bin/protomol +bin/xyzviz +%%PORTDOCS%%%%EXAMPLESDIR%%/coulomb_309/309ca.config +%%PORTDOCS%%%%EXAMPLESDIR%%/coulomb_309/309ca.par +%%PORTDOCS%%%%EXAMPLESDIR%%/coulomb_309/309ca.pos.xyz +%%PORTDOCS%%%%EXAMPLESDIR%%/coulomb_309/309ca.psf +%%PORTDOCS%%%%EXAMPLESDIR%%/alanine_dipeptide_water_184x/alanine.equil.psf +%%PORTDOCS%%%%EXAMPLESDIR%%/alanine_dipeptide_water_184x/alanine.7ns.namd +%%PORTDOCS%%%%EXAMPLESDIR%%/alanine_dipeptide_water_184x/alanine.equil.pdb +%%PORTDOCS%%%%EXAMPLESDIR%%/alanine_dipeptide_water_184x/ala607.pgn +%%PORTDOCS%%%%EXAMPLESDIR%%/alanine_dipeptide_water_184x/alanine.namd +%%PORTDOCS%%%%EXAMPLESDIR%%/alanine_dipeptide_water_184x/alanine.pdb +%%PORTDOCS%%%%EXAMPLESDIR%%/alanine_dipeptide_water_184x/alanine.psf +%%PORTDOCS%%%%EXAMPLESDIR%%/argon_400/argon.par +%%PORTDOCS%%%%EXAMPLESDIR%%/argon_400/argon.lf.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/argon_400/argon.npt.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/argon_400/argon.pdb +%%PORTDOCS%%%%EXAMPLESDIR%%/argon_400/argon.psf +%%PORTDOCS%%%%EXAMPLESDIR%%/argon_400/argon.vel.pdb +%%PORTDOCS%%%%EXAMPLESDIR%%/bpti_water_1101/bpti.par +%%PORTDOCS%%%%EXAMPLESDIR%%/bpti_water_1101/bpti.hmc.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/bpti_water_1101/bpti.lf.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/bpti_water_1101/bpti.pdb +%%PORTDOCS%%%%EXAMPLESDIR%%/bpti_water_1101/bpti.psf +%%PORTDOCS%%%%EXAMPLESDIR%%/bpti_water_1101/bpti.shmc.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/bpti_water_14281/bpti.shake.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/bpti_water_14281/bpti.ewald.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/bpti_water_14281/bpti.mg.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/bpti_water_14281/bpti.namd +%%PORTDOCS%%%%EXAMPLESDIR%%/bpti_water_14281/bpti.par +%%PORTDOCS%%%%EXAMPLESDIR%%/bpti_water_14281/bpti.pbc.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/bpti_water_14281/bpti.pdb +%%PORTDOCS%%%%EXAMPLESDIR%%/bpti_water_14281/bpti.psf +%%PORTDOCS%%%%EXAMPLESDIR%%/butane_4/runButaneTests.sh +%%PORTDOCS%%%%EXAMPLESDIR%%/butane_4/README +%%PORTDOCS%%%%EXAMPLESDIR%%/butane_4/UA_butane.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/butane_4/UA_butane.dhmc.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/butane_4/UA_butane.hmc.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/butane_4/UA_butane.lf.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/butane_4/UA_butane.par +%%PORTDOCS%%%%EXAMPLESDIR%%/butane_4/UA_butane.pdb +%%PORTDOCS%%%%EXAMPLESDIR%%/butane_4/UA_butane.psf +%%PORTDOCS%%%%EXAMPLESDIR%%/butane_4/angleSetDHMC +%%PORTDOCS%%%%EXAMPLESDIR%%/butane_4/cleanOutput.bash +%%PORTDOCS%%%%EXAMPLESDIR%%/butane_4/dihedralSetDHMC +%%PORTDOCS%%%%EXAMPLESDIR%%/butane_4/procDihedralFile.awk +%%PORTDOCS%%%%EXAMPLESDIR%%/butane_4/runButaneResults.sh +%%PORTDOCS%%%%EXAMPLESDIR%%/alanine_dipeptide_23/ala_equil.pdb +%%PORTDOCS%%%%EXAMPLESDIR%%/alanine_dipeptide_23/ala_equil.psf +%%PORTDOCS%%%%EXAMPLESDIR%%/alanine_dipeptide_23/ala_equilibrated.pdb +%%PORTDOCS%%%%EXAMPLESDIR%%/alanine_dipeptide_23/ala_equilibrated.pgn +%%PORTDOCS%%%%EXAMPLESDIR%%/decalanine_66/dihedralIndexSet +%%PORTDOCS%%%%EXAMPLESDIR%%/decalanine_66/alanine.BSplineMOLLY.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/decalanine_66/alanine.Equilibrium.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/decalanine_66/alanine.LF.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/decalanine_66/alanine.LFwDihedralOut.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/decalanine_66/alanine.PLF.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/decalanine_66/alanine.Shake.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/decalanine_66/alanine.par +%%PORTDOCS%%%%EXAMPLESDIR%%/decalanine_66/alanine.pdb +%%PORTDOCS%%%%EXAMPLESDIR%%/decalanine_66/alanine.psf +%%PORTDOCS%%%%EXAMPLESDIR%%/decalanine_66/alanine.testSet +%%PORTDOCS%%%%EXAMPLESDIR%%/decalanine_66/alanine.water.pdb +%%PORTDOCS%%%%EXAMPLESDIR%%/decalanine_66/alanine.water.psf +%%PORTDOCS%%%%EXAMPLESDIR%%/electrons_22/22el.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/electrons_22/22el.pos.xyz +%%PORTDOCS%%%%EXAMPLESDIR%%/electrons_22/22el.psf +%%PORTDOCS%%%%EXAMPLESDIR%%/electrons_22/22el.vel.xyz +%%PORTDOCS%%%%EXAMPLESDIR%%/electrons_22/el.par +%%PORTDOCS%%%%EXAMPLESDIR%%/methane_ethane_xxx/iSGMD_README +%%PORTDOCS%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane.par +%%PORTDOCS%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane.trans +%%PORTDOCS%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_100.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_100_Pure_Trappe.coor.xyz +%%PORTDOCS%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_100_Pure_Trappe.psf +%%PORTDOCS%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_100_Pure_Trappe.vel.xyz +%%PORTDOCS%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_100_Pure_Trappe.xsc +%%PORTDOCS%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_300.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_300_Pure_Trappe.coor.xyz +%%PORTDOCS%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_300_Pure_Trappe.psf +%%PORTDOCS%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_300_Pure_Trappe.vel.xyz +%%PORTDOCS%%%%EXAMPLESDIR%%/methane_ethane_xxx/ethane_methane_300_Pure_Trappe.xsc +%%PORTDOCS%%%%EXAMPLESDIR%%/testset/test.tcsh +%%PORTDOCS%%%%EXAMPLESDIR%%/testset/README +%%PORTDOCS%%%%EXAMPLESDIR%%/testset/hmc.Bsp_PME.pb.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/testset/hmc.std.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/testset/lf.Ewald.pb.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/testset/lf.MG.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/testset/lf.PME.pb.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/testset/lf.std.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/testset/lf.std.pb.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/testset/shmc.Bsp_PME.pb.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/testset/shmc.std.pb.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/testset/slf.std.pb.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/water_216/water216.vel.pdb +%%PORTDOCS%%%%EXAMPLESDIR%%/water_216/water216.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/water_216/water216.coor.pdb +%%PORTDOCS%%%%EXAMPLESDIR%%/water_216/water216.new.pos.pdb +%%PORTDOCS%%%%EXAMPLESDIR%%/water_216/water216.new.vel.pdb +%%PORTDOCS%%%%EXAMPLESDIR%%/water_216/water216.par +%%PORTDOCS%%%%EXAMPLESDIR%%/water_216/water216.psf +%%PORTDOCS%%%%EXAMPLESDIR%%/water_648/water648.tip3.psf +%%PORTDOCS%%%%EXAMPLESDIR%%/water_648/water648.fluid.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/water_648/water648.fluid.pos.xyz +%%PORTDOCS%%%%EXAMPLESDIR%%/water_648/water648.ice.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/water_648/water648.ice.nvt.conf +%%PORTDOCS%%%%EXAMPLESDIR%%/water_648/water648.ice.pos.xyz +%%PORTDOCS%%%%EXAMPLESDIR%%/water_648/water648.spce.par +%%PORTDOCS%%%%EXAMPLESDIR%%/water_648/water648.spce.psf +%%PORTDOCS%%%%EXAMPLESDIR%%/water_648/water648.tip3.par +%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/coulomb_309 +%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/alanine_dipeptide_water_184x +%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/argon_400 +%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/bpti_water_1101 +%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/bpti_water_14281 +%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/butane_4 +%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/alanine_dipeptide_23 +%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/decalanine_66 +%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/electrons_22 +%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/methane_ethane_xxx +%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/testset +%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/water_216 +%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/water_648 +%%PORTDOCS%%@dirrm %%EXAMPLESDIR%% -- cgit