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Code Issues Releases Activity

Update tinker from version 3.6 to version 3.7

Browse Source 
PR:	12301
Submitted by:	maintainer
This commit is contained in:
Chris Piazza 1999-06-23 00:26:02 +00:00
parent 7d1e7b5a76
commit d782b1db2a
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=19700
7 changed files with 289 additions and 310 deletions
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26
biology/tinker/Makefile
View File

@ -1,13 +1,13 @@
# New ports collection makefile for: tinker
# Version required: 3.6
# Version required: 3.7
# Date Created: 26 August 1998
# Whom: Glenn Johnson
#
# $Id: Makefile,v 1.2 1998/11/18 02:10:54 jkoshy Exp $
# $Id: Makefile,v 1.3 1999/05/24 02:01:37 steve Exp $
#
DISTNAME= tinker
PKGNAME= tinker-3.6
PKGNAME= tinker-3.7
CATEGORIES= biology
MASTER_SITES= ftp://dasher.wustl.edu/pub/
@ -18,12 +18,15 @@ MAINTAINER= gjohnson@nola.srrc.usda.gov
.if ${OSVERSION} < 400005
LIB_DEPENDS= U77:${PORTSDIR}/devel/libU77
# If you have EGCS installed and wish to use it, do the following:
# If you wish to use g77 from EGCS, do the following:
# a) comment out the LIB_DEPENDS line above and uncomment the following line
#BUILD_DEPENDS= g77:${PORTSDIR}/lang/egcs
# b) set env variable 'FC' to 'g77' before running `make'
# BUILD_DEPENDS= g77:${PORTSDIR}/lang/egcs
# b) set env variable 'FC' to 'g77' before running `make'; or 'make FC=g77'
.else
MAKE_ENV+= HAVE_G2C=yes
MAKE_ENV+= HAVE_G2C=yes INSTALL_PROGRAM="${INSTALL_PROGRAM}"
.endif
WRKSRC= ${WRKDIR}/tinker/source
@ -35,17 +38,20 @@ INSTALL_TARGET= rename
RESTRICTED= author requests no distribution except from his FTP site
post-install:
${MKDIR} ${PREFIX}/share/tinker
${MKDIR} ${PREFIX}/share/tinker/params
${INSTALL_DATA} ${WRKDIR}/tinker/params/* \
${PREFIX}/share/tinker/params
${INSTALL_DATA} ${WRKDIR}/tinker/source/tinker.txt \
${PREFIX}/share/tinker
${INSTALL_DATA} ${WRKDIR}/tinker/params/* \
${PREFIX}/share/tinker/params
.if !defined(NOPORTDOCS)
${MKDIR} ${PREFIX}/share/tinker/doc
${MKDIR} ${PREFIX}/share/tinker/example
${MKDIR} ${PREFIX}/share/tinker/bench
${MKDIR} ${PREFIX}/share/tinker/test
${INSTALL_DATA} ${WRKDIR}/tinker/doc/README \
${PREFIX}/share/tinker/doc
${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.pdf \
${PREFIX}/share/tinker/doc
${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.ps \
${PREFIX}/share/tinker/doc
@ -96,7 +102,7 @@ ${PREFIX}/share/tinker/bench
@${ECHO} ""
@${ECHO} " **********************************************************"
@${ECHO} " The author requests that you return a license form "
@${ECHO} " to him if you find Tinker to be useful. "
@${ECHO} " to him if you find Tinker to be useful. "
@${ECHO} " "
@${ECHO} " See ${PREFIX}/share/tinker/doc for license forms. "
@${ECHO} " **********************************************************"

2
biology/tinker/distinfo
View File

@ -1 +1 @@
MD5 (tinker.tar.gz) = 9b21715ee725eddbcd750a1d0f5836b4
MD5 (tinker.tar.gz) = 1b05697908aecb88aee9054188f8ac7f

416
biology/tinker/files/patch-aa
View File

@ -1,225 +1,191 @@
*** ../make/Makefile.orig Sat Apr 11 11:38:14 1998
--- ../make/Makefile Sat May 22 15:08:09 1999
***************
*** 9,16 ****
##
## 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
## 6. make listing Concatenate source to tinker.txt
## 5. make clean Delete objects and executables
##
--- 9,16 ----
##
## 1. make all Build all the TINKER executables
## 2. make rename Move the executables to BINDIR
! ## 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
##
***************
*** 30,38 ****
## LINKDIR Linked Copies of TINKER Executables
##
! TINKERDIR = /user/ponder/tinker
! BINDIR = $(TINKERDIR)/bin
! LINKDIR = /usr/local/bin
####################################################################
## Known Machine Types; Uncomment One of the Following Sections ##
--- 30,38 ----
## LINKDIR Linked Copies of TINKER Executables
##
! TINKERDIR = ${WRKDIR}
! BINDIR = ${PREFIX}/bin
! #LINKDIR = /usr/local/bin
####################################################################
## Known Machine Types; Uncomment One of the Following Sections ##
***************
*** 45,57 ****
## Compiler: DEC Fortran 77/90, V4.1
##
! F77 = /usr/bin/f77
! RM = /sbin/rm
! LIBS =
! F77FLAGS = -c
! OPTFLAGS = -fast -tune host
! LIBFLAGS = -rlv
! LINKFLAGS = -fast -non_shared -om -WL,-om_no_inst_sched
##
## Machine: Silicon Graphics
--- 45,57 ----
## Compiler: DEC Fortran 77/90, V4.1
##
! #F77 = /usr/bin/f77
! #RM = /sbin/rm
! #LIBS =
! #F77FLAGS = -c
! #OPTFLAGS = -fast -tune host
! #LIBFLAGS = -rlv
! #LINKFLAGS = -fast -non_shared -om -WL,-om_no_inst_sched
##
## Machine: Silicon Graphics
***************
*** 104,109 ****
--- 104,141 ----
#diagq.o:
# ${F77} ${F77FLAGS} -ffast-math diagq.f
+ ##
+ ## Machine: IntelPC
+ ## CPU Type: Pentium Pro
+ ## Oper Sys: FreeBSD 3.0
+ ## Compiler: f77(f2c/gcc version 2.7.2.1) || egcs g77
+ ##
+
+ F77 = ${FC}
+ RM = /bin/rm
+
+ .if ${FC}==f77
+ .if !defined(HAVE_G2C)
+ LIBS = -lU77
+ .else
+ LIBS = -lg2c
+ .endif
+ F77FLAGS = -NL400 -c
+ LINKFLAGS = -L${PREFIX}/lib
+ .elseif ${FC}==g77
+ LIBS=
+ F77FLAGS = -Wno-globals -fno-globals -c
+ LINKFLAGS =
+ .endif
+
+ OPTFLAGS = ${FFLAGS} -ffast-math
+ .if ${MACHINE_ARCH} == "i386"
+ OPTFLAGS+= -malign-double
+ .endif
+ LIBFLAGS = -rcuv
+ diagq.o:
+ ${F77} ${F77FLAGS} -ffast-math diagq.f
+
#################################################################
## Should not be Necessary to Change Things Below this Point ##
#################################################################
***************
*** 766,771 ****
--- 798,804 ----
volume2.o \
writeout.o \
xyzatm.o
+ ranlib libtinker.a
alchemy.x:
${F77} ${LINKFLAGS} -o alchemy.x alchemy.o libtinker.a ${LIBS}
***************
*** 857,906 ****
${F77} ${LINKFLAGS} -o xyzsybyl.x xyzsybyl.o libtinker.a ${LIBS}
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 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 newton.x $(BINDIR)/newton
! mv newtrot.x $(BINDIR)/newtrot
! 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 protein.x $(BINDIR)/protein
! mv pss.x $(BINDIR)/pss
! mv pssrigid.x $(BINDIR)/pssrigid
! mv pssrot.x $(BINDIR)/pssrot
! mv saddle.x $(BINDIR)/saddle
! mv sniffer.x $(BINDIR)/sniffer
! mv spacefill.x $(BINDIR)/spacefill
! mv superpose.x $(BINDIR)/superpose
! mv sybylxyz.x $(BINDIR)/sybylxyz
! mv testgrad.x $(BINDIR)/testgrad
! mv testhess.x $(BINDIR)/testhess
! mv testlight.x $(BINDIR)/testlight
! mv testrot.x $(BINDIR)/testrot
! mv timer.x $(BINDIR)/timer
! mv timerot.x $(BINDIR)/timerot
! 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
remove_links:
rm -f $(LINKDIR)/alchemy
--- 890,939 ----
${F77} ${LINKFLAGS} -o xyzsybyl.x xyzsybyl.o libtinker.a ${LIBS}
rename:
! ${INSTALL} -s alchemy.x $(BINDIR)/alchemy
! ${INSTALL} -s analyze.x $(BINDIR)/analyze
! ${INSTALL} -s anneal.x $(BINDIR)/anneal
! ${INSTALL} -s archive.x $(BINDIR)/archive
! ${INSTALL} -s correlate.x $(BINDIR)/correlate
! ${INSTALL} -s crystal.x $(BINDIR)/crystal
! ${INSTALL} -s distgeom.x $(BINDIR)/distgeom
! ${INSTALL} -s document.x $(BINDIR)/document
! ${INSTALL} -s dynamic.x $(BINDIR)/dynamic
! ${INSTALL} -s gda.x $(BINDIR)/gda
! ${INSTALL} -s intedit.x $(BINDIR)/intedit
! ${INSTALL} -s intxyz.x $(BINDIR)/intxyz
! ${INSTALL} -s minimize.x $(BINDIR)/minimize
! ${INSTALL} -s minirot.x $(BINDIR)/minirot
! ${INSTALL} -s newton.x $(BINDIR)/newton
! ${INSTALL} -s newtrot.x $(BINDIR)/newtrot
! ${INSTALL} -s optimize.x $(BINDIR)/optimize
! ${INSTALL} -s optirot.x $(BINDIR)/optirot
! ${INSTALL} -s optrigid.x $(BINDIR)/optrigid
! ${INSTALL} -s path.x $(BINDIR)/path
! ${INSTALL} -s pdbxyz.x $(BINDIR)/pdbxyz
! ${INSTALL} -s protein.x $(BINDIR)/protein
! ${INSTALL} -s pss.x $(BINDIR)/pss
! ${INSTALL} -s pssrigid.x $(BINDIR)/pssrigid
! ${INSTALL} -s pssrot.x $(BINDIR)/pssrot
! ${INSTALL} -s saddle.x $(BINDIR)/saddle
! ${INSTALL} -s sniffer.x $(BINDIR)/sniffer
! ${INSTALL} -s spacefill.x $(BINDIR)/spacefill
! ${INSTALL} -s superpose.x $(BINDIR)/superpose
! ${INSTALL} -s sybylxyz.x $(BINDIR)/sybylxyz
! ${INSTALL} -s testgrad.x $(BINDIR)/testgrad
! ${INSTALL} -s testhess.x $(BINDIR)/testhess
! ${INSTALL} -s testlight.x $(BINDIR)/testlight
! ${INSTALL} -s testrot.x $(BINDIR)/testrot
! ${INSTALL} -s timer.x $(BINDIR)/timer
! ${INSTALL} -s timerot.x $(BINDIR)/timerot
! ${INSTALL} -s vibrate.x $(BINDIR)/vibrate
! ${INSTALL} -s vibrot.x $(BINDIR)/vibrot
! ${INSTALL} -s xtalfit.x $(BINDIR)/xtalfit
! ${INSTALL} -s xtalmin.x $(BINDIR)/xtalmin
! ${INSTALL} -s xyzedit.x $(BINDIR)/xyzedit
! ${INSTALL} -s xyzint.x $(BINDIR)/xyzint
! ${INSTALL} -s xyzpdb.x $(BINDIR)/xyzpdb
! ${INSTALL} -s xyzsybyl.x $(BINDIR)/xyzsybyl
remove_links:
rm -f $(LINKDIR)/alchemy
--- ../make/Makefile.orig Mon Jun 14 08:23:04 1999
+++ ../make/Makefile Tue Jun 22 17:13:26 1999
@@ -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 = /user/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 ##
@@ -45,13 +45,13 @@
## Compiler: DEC Fortran 77/90, V4.1
##
-F77 = /usr/bin/f77
-RM = /sbin/rm
-LIBS =
-F77FLAGS = -c
-OPTFLAGS = -fast -tune host
-LIBFLAGS = -rlv
-LINKFLAGS = -fast -non_shared -om -WL,-om_no_inst_sched
+#F77 = /usr/bin/f77
+#RM = /sbin/rm
+#LIBS =
+#F77FLAGS = -c
+#OPTFLAGS = -fast -tune host
+#LIBFLAGS = -rlv
+#LINKFLAGS = -fast -non_shared -om -WL,-om_no_inst_sched
##
## Machine: Silicon Graphics
@@ -104,6 +104,38 @@
#diagq.o:
# ${F77} ${F77FLAGS} -ffast-math diagq.f
+##
+## Machine: IntelPC
+## CPU Type: Pentium Pro
+## Oper Sys: FreeBSD 3.0
+## Compiler: f77(f2c/gcc version 2.7.2.1) || egcs g77
+##
+
+F77 = ${FC}
+RM = /bin/rm
+
+.if ${FC}==f77
+.if !defined(HAVE_G2C)
+LIBS = -lU77
+.else
+LIBS = -lg2c
+.endif
+F77FLAGS = -NL400 -c
+LINKFLAGS = -L${PREFIX}/lib
+.elseif ${FC}==g77
+LIBS=
+F77FLAGS = -Wno-globals -fno-globals -c
+LINKFLAGS =
+.endif
+
+OPTFLAGS = ${FFLAGS} -ffast-math
+.if ${MACHINE_ARCH} == "i386"
+OPTFLAGS+= -malign-double
+.endif
+LIBFLAGS = -rcuv
+diagq.o:
+ ${F77} ${F77FLAGS} -ffast-math diagq.f
+
#################################################################
## Should not be Necessary to Change Things Below this Point ##
#################################################################
@@ -765,6 +797,7 @@
volume2.o \
writeout.o \
xyzatm.o
+ ranlib libtinker.a
alchemy.x:
${F77} ${LINKFLAGS} -o alchemy.x alchemy.o libtinker.a ${LIBS}
@@ -858,51 +891,51 @@
${F77} ${LINKFLAGS} -o xyzsybyl.x xyzsybyl.o libtinker.a ${LIBS}
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 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 newton.x $(BINDIR)/newton
- mv newtrot.x $(BINDIR)/newtrot
- 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 protein.x $(BINDIR)/protein
- mv pss.x $(BINDIR)/pss
- mv pssrigid.x $(BINDIR)/pssrigid
- mv pssrot.x $(BINDIR)/pssrot
- mv saddle.x $(BINDIR)/saddle
- mv scan.x $(BINDIR)/scan
- mv sniffer.x $(BINDIR)/sniffer
- mv spacefill.x $(BINDIR)/spacefill
- mv superpose.x $(BINDIR)/superpose
- mv sybylxyz.x $(BINDIR)/sybylxyz
- mv testgrad.x $(BINDIR)/testgrad
- mv testhess.x $(BINDIR)/testhess
- mv testlight.x $(BINDIR)/testlight
- mv testrot.x $(BINDIR)/testrot
- mv timer.x $(BINDIR)/timer
- mv timerot.x $(BINDIR)/timerot
- 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} 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} newton.x $(BINDIR)/newton
+ ${INSTALL_PROGRAM} newtrot.x $(BINDIR)/newtrot
+ ${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} protein.x $(BINDIR)/protein
+ ${INSTALL_PROGRAM} pss.x $(BINDIR)/pss
+ ${INSTALL_PROGRAM} pssrigid.x $(BINDIR)/pssrigid
+ ${INSTALL_PROGRAM} pssrot.x $(BINDIR)/pssrot
+ ${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} superpose.x $(BINDIR)/superpose
+ ${INSTALL_PROGRAM} sybylxyz.x $(BINDIR)/sybylxyz
+ ${INSTALL_PROGRAM} testgrad.x $(BINDIR)/testgrad
+ ${INSTALL_PROGRAM} testhess.x $(BINDIR)/testhess
+ ${INSTALL_PROGRAM} testlight.x $(BINDIR)/testlight
+ ${INSTALL_PROGRAM} testrot.x $(BINDIR)/testrot
+ ${INSTALL_PROGRAM} timer.x $(BINDIR)/timer
+ ${INSTALL_PROGRAM} timerot.x $(BINDIR)/timerot
+ ${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

31
biology/tinker/files/patch-ab
View File

@ -1,19 +1,12 @@
*** ../doc/license.txt.orig Fri Aug 28 23:47:07 1998
--- ../doc/license.txt Fri Aug 28 23:49:13 1998
***************
*** 1,7 ****
! TINKER ­ Software Tools for Molecular Design
Version 3.6 February 1998
! Copyright © 1990-1998 Jay William Ponder
TINKER is a modular program package for molecular mechanics-
based potential energy calculations, molecular dynamics
--- 1,7 ----
! TINKER -- Software Tools for Molecular Design
Version 3.6 February 1998
! Copyright 1990-1998 Jay William Ponder
TINKER is a modular program package for molecular mechanics-
based potential energy calculations, molecular dynamics
--- ../doc/license.txt.orig Wed Jun 16 13:54:43 1999
+++ ../doc/license.txt Sat Jun 19 14:19:18 1999
@@ -1,7 +1,7 @@
- TINKER ­ Software Tools for Molecular Design
+ TINKER - Software Tools for Molecular Design
Version 3.7 June 1999
- Copyright © 1990-1999 Jay William Ponder
+ Copyright (c) 1990-1999 Jay William Ponder
TINKER is a modular program package for molecular mechanics-
based potential energy calculations, molecular dynamics

2
biology/tinker/files/patch-ac
View File

@ -7,7 +7,7 @@
Jay Ponder Lab, Dept. of Biochemistry & Molecular
Biophysics,
--- 1,4 ----
! TINKER -- Software Tools for Molecular Design
! TINKER - Software Tools for Molecular Design
Jay Ponder Lab, Dept. of Biochemistry & Molecular
Biophysics,

9
biology/tinker/pkg-descr
View File

@ -1,10 +1,11 @@
Tinker is a set of small programs for doing general purpose molecular
modeling. Tools are included for energy minimizations, geometry
calculations, and molecular analysis calculations. Tools for
converting coordinate sets are also provided.
calculations, and molecular analysis calculations. Tools for converting
coordinate sets are also provided.
Tinker employs several force fields and minimizaation techniques.
Simulated annealing and molecular dynamics can be performed with
Tinker.
Simulated annealing and molecular dynamics can be performed with Tinker.
For more information about Tinker see:
WWW: http://dasher.wustl.edu/tinker/

113
biology/tinker/pkg-plist
View File

@ -24,6 +24,7 @@ bin/pss
bin/pssrigid
bin/pssrot
bin/saddle
bin/scan
bin/sniffer
bin/spacefill
bin/superpose
@ -42,31 +43,40 @@ bin/xyzedit
bin/xyzint
bin/xyzpdb
bin/xyzsybyl
share/tinker/params/README
share/tinker/params/amber.prm
share/tinker/params/charmm.prm
share/tinker/params/emr.prm
share/tinker/params/hoch.prm
share/tinker/params/merck.prm
share/tinker/params/mm2.prm
share/tinker/params/mm3.prm
share/tinker/params/mm3pro.prm
share/tinker/params/mmffpro.prm
share/tinker/params/opls.prm
share/tinker/params/oplsaa.prm
share/tinker/params/smooth.prm
share/tinker/params/tinker.prm
share/tinker/params/water.prm
share/tinker/bench/crambin.input
share/tinker/bench/crambin.key
share/tinker/bench/crambin.run
share/tinker/bench/crambin.xyz
share/tinker/bench/crystal.input
share/tinker/bench/crystal.key
share/tinker/bench/crystal.run
share/tinker/bench/crystal.xyz
share/tinker/bench/results-2.3
share/tinker/bench/results-2.4
share/tinker/bench/results-2.9
share/tinker/bench/results-3.1
share/tinker/bench/results-3.2
share/tinker/bench/results-3.4
share/tinker/bench/results-3.5
share/tinker/bench/results-3.7
share/tinker/bench/water.dyn0
share/tinker/bench/water.input
share/tinker/bench/water.key
share/tinker/bench/water.run
share/tinker/bench/water.xyz
share/tinker/doc/README
share/tinker/doc/guide.pdf
share/tinker/doc/guide.ps.Z
share/tinker/doc/guide.txt
share/tinker/doc/license.pdf
share/tinker/doc/license.ps
share/tinker/doc/license.txt
share/tinker/doc/logo-bind.ps.Z
share/tinker/doc/logo.ps.Z
share/tinker/doc/spine.ps
share/tinker/doc/summary.pdf
share/tinker/doc/summary.ps
share/tinker/doc/summary.txt
share/tinker/tinker.txt
share/tinker/example/README
share/tinker/example/anion.dyn0
share/tinker/example/anion.in1
@ -116,26 +126,25 @@ share/tinker/example/formamide.in4
share/tinker/example/formamide.key
share/tinker/example/formamide.log
share/tinker/example/formamide.run
share/tinker/bench/crambin.input
share/tinker/bench/crambin.key
share/tinker/bench/crambin.run
share/tinker/bench/crambin.xyz
share/tinker/bench/crystal.input
share/tinker/bench/crystal.key
share/tinker/bench/crystal.run
share/tinker/bench/crystal.xyz
share/tinker/bench/results-2.3
share/tinker/bench/results-2.4
share/tinker/bench/results-2.9
share/tinker/bench/results-3.1
share/tinker/bench/results-3.2
share/tinker/bench/results-3.4
share/tinker/bench/results-3.5
share/tinker/bench/water.dyn0
share/tinker/bench/water.input
share/tinker/bench/water.key
share/tinker/bench/water.run
share/tinker/bench/water.xyz
share/tinker/example/helix.in1
share/tinker/example/helix.key
share/tinker/example/helix.log
share/tinker/example/helix.run
share/tinker/example/helix.xyz
share/tinker/params/README
share/tinker/params/amber.prm
share/tinker/params/charmm.prm
share/tinker/params/emr.prm
share/tinker/params/hoch.prm
share/tinker/params/mm2.prm
share/tinker/params/mm3.prm
share/tinker/params/mm3pro.prm
share/tinker/params/opls.prm
share/tinker/params/oplsaa.prm
share/tinker/params/smooth.prm
share/tinker/params/smoothaa.prm
share/tinker/params/tinker.prm
share/tinker/params/water.prm
share/tinker/test/README
share/tinker/test/ala20.key
share/tinker/test/ala20.xyz
@ -148,15 +157,16 @@ share/tinker/test/annulene3.key
share/tinker/test/annulene3.xyz
share/tinker/test/arach.int
share/tinker/test/arach.key
share/tinker/test/arach.xmol
share/tinker/test/arach.xyz
share/tinker/test/azulene.int
share/tinker/test/azulene.key
share/tinker/test/azulene.xyz
share/tinker/test/bearing.big
share/tinker/test/bearing.key
share/tinker/test/bearing.pdb
share/tinker/test/bearing.xyz
share/tinker/test/bearing2.key
share/tinker/test/bearing2.pdb
share/tinker/test/bearing2.xyz
share/tinker/test/benzene.int
share/tinker/test/benzene.key
share/tinker/test/benzene.xyz
@ -177,29 +187,30 @@ share/tinker/test/butopls.xyz
share/tinker/test/butopls2.int
share/tinker/test/butopls2.key
share/tinker/test/butopls2.xyz
share/tinker/test/c5.int
share/tinker/test/c5.key
share/tinker/test/c5.seq
share/tinker/test/c5.xyz
share/tinker/test/c7ax.int
share/tinker/test/c7ax.key
share/tinker/test/c7ax.seq
share/tinker/test/c7ax.xyz
share/tinker/test/c7eq.int
share/tinker/test/c7eq.key
share/tinker/test/c7eq.seq
share/tinker/test/c7eq.xyz
share/tinker/test/cpentene.key
share/tinker/test/cpentene.xyz
share/tinker/test/crambin.int
share/tinker/test/crambin.key
share/tinker/test/crambin.pdb
share/tinker/test/crambin.seq
share/tinker/test/crambin.xyz
share/tinker/test/crambinx.key
share/tinker/test/crambinx.ray
share/tinker/test/crambinx.xyz
share/tinker/test/crown.int
share/tinker/test/crown.key
share/tinker/test/crown.xyz
share/tinker/test/cychept.int
share/tinker/test/cychept.key
share/tinker/test/cychept.pdb
share/tinker/test/cychept.xyz
share/tinker/test/cyclo.int
share/tinker/test/cyclo.key
@ -207,24 +218,26 @@ share/tinker/test/cyclo.xyz
share/tinker/test/cyclo2.int
share/tinker/test/cyclo2.key
share/tinker/test/cyclo2.xyz
share/tinker/test/nma.int
share/tinker/test/diene.int
share/tinker/test/diene.key
share/tinker/test/diene.xyz
share/tinker/test/dimethane.key
share/tinker/test/dimethane.xyz
share/tinker/test/diwater.key
share/tinker/test/diwater.lin
share/tinker/test/diwater.min
share/tinker/test/diwater.xyz
share/tinker/test/enkephalin.int
share/tinker/test/enkephalin.key
share/tinker/test/enkephalin.make
share/tinker/test/enkephalin.pdb
share/tinker/test/enkephalin.run
share/tinker/test/enkephalin.seq
share/tinker/test/enkephalin.xyz
share/tinker/test/ermer.int
share/tinker/test/ermer.key
share/tinker/test/ermer.xyz
share/tinker/test/ester.key
share/tinker/test/ester.xyz
share/tinker/test/ethane.int
share/tinker/test/ethane.key
share/tinker/test/ethane.xyz
@ -234,6 +247,8 @@ share/tinker/test/ethylene.xyz
share/tinker/test/flane.int
share/tinker/test/flane.key
share/tinker/test/flane.xyz
share/tinker/test/formamide.key
share/tinker/test/formamide.xyz
share/tinker/test/furan.int
share/tinker/test/furan.key
share/tinker/test/furan.xyz
@ -254,6 +269,7 @@ share/tinker/test/methane.key
share/tinker/test/methane.xyz
share/tinker/test/methanol.key
share/tinker/test/methanol.xyz
share/tinker/test/nma.int
share/tinker/test/nma.key
share/tinker/test/nma.xyz
share/tinker/test/nmabox.dyn
@ -280,10 +296,6 @@ share/tinker/test/peptide.seq
share/tinker/test/peptide.xyz
share/tinker/test/phenanth.key
share/tinker/test/phenanth.xyz
share/tinker/test/photo.key
share/tinker/test/photo.pdb
share/tinker/test/photo.seq
share/tinker/test/photo.xyz
share/tinker/test/propellane.int
share/tinker/test/propellane.key
share/tinker/test/propellane.xyz
@ -328,9 +340,10 @@ share/tinker/test/watersmall.xyz
share/tinker/test/white.int
share/tinker/test/white.key
share/tinker/test/white.xyz
@dirrm share/tinker/params
share/tinker/tinker.txt
@dirrm share/tinker/bench
@dirrm share/tinker/doc
@dirrm share/tinker/example
@dirrm share/tinker/bench
@dirrm share/tinker/params
@dirrm share/tinker/test
@dirrm share/tinker