Date: Thu, 30 Mar 2006 19:07:16 GMT From: Sangwoo Shim <sangwoos@gmail.com> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/95123: New port: biology/protomol Message-ID: <200603301907.k2UJ7G3X076867@www.freebsd.org> Resent-Message-ID: <200603301910.k2UJACw2084141@freefall.freebsd.org>
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>Number: 95123
>Category: ports
>Synopsis: New port: biology/protomol
>Confidential: no
>Severity: non-critical
>Priority: medium
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: update
>Submitter-Id: current-users
>Arrival-Date: Thu Mar 30 19:10:12 GMT 2006
>Closed-Date:
>Last-Modified:
>Originator: Sangwoo Shim
>Release: FreeBSD 6.1-PRERELEASE
>Organization:
Seoul Natl' Univ.
>Environment:
FreeBSD rumba.swoo.org 6.1-PRERELEASE FreeBSD 6.1-PRERELEASE #2: Tue Mar 14 09:52:40 KST 2006 root@rumba.swoo.org:/usr/obj/usr/src/sys/SWOO i386
>Description:
ProtoMol is an object-oriented, component based, framework for molecular dynamics (MD) simulations. I made a port for this program to use it on FreeBSD.
I'm willing to be the maintainer of this port.
>How-To-Repeat:
>Fix:
diff -urN protomol.empty/Makefile protomol/Makefile
--- protomol.empty/Makefile Thu Jan 1 09:00:00 1970
+++ protomol/Makefile Fri Mar 31 03:52:49 2006
@@ -0,0 +1,23 @@
+PORTNAME= protomol
+PORTVERSION= 2.0.3
+CATEGORIES= biology
+MASTER_SITES= ${MASTER_SITE_SOURCEFORGE}
+MASTER_SITE_SUBDIR= ${PORTNAME}
+DISTNAME= ${PORTNAME}
+DISTFILES= ${PORTNAME}-${PORTVERSION}-tar.gz
+
+MAINTAINER= sangwoos@gmail.com
+COMMENT= ProtoMol is an object-oriented, component based, framework for molecular dynamics (MD) simulations.
+
+GNU_CONFIGURE= yes
+# Hack to cure a misbehavior of the configure script.
+CONFIGURE_ARGS+= --without-irix_mipspro_mpi
+
+post-install:
+.if !defined(NOPORTDOCS)
+ @${MKDIR} ${EXAMPLESDIR}
+ cd ${WRKSRC}/examples && ${FIND} . | ${EGREP} -v '\.cvsignore' | \
+ ${CPIO} -pdmu -R ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
+.endif
+
+.include <bsd.port.mk>
diff -urN protomol.empty/distinfo protomol/distinfo
--- protomol.empty/distinfo Thu Jan 1 09:00:00 1970
+++ protomol/distinfo Fri Mar 31 02:00:24 2006
@@ -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 -urN protomol.empty/pkg-descr protomol/pkg-descr
--- protomol.empty/pkg-descr Thu Jan 1 09:00:00 1970
+++ protomol/pkg-descr Fri Mar 31 03:27:54 2006
@@ -0,0 +1,16 @@
+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 -urN protomol.empty/pkg-plist protomol/pkg-plist
--- protomol.empty/pkg-plist Thu Jan 1 09:00:00 1970
+++ protomol/pkg-plist Fri Mar 31 03:58:20 2006
@@ -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%%
>Release-Note:
>Audit-Trail:
>Unformatted:
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