New port of the Tinker Molecular modelling program.

PR:		8690
Reviewed by:	jkoshy
Submitted by:	Glenn Johnson <gljohns@bellsouth.net>

11 files changed, 725 insertions, 0 deletions

diff --git a/biology/tinker/Makefile b/biology/tinker/Makefile
new file mode 100644
index 000000000000..ba4dc0399118
--- /dev/null
+++ b/biology/tinker/Makefile
@@ -0,0 +1,100 @@
+# New ports collection makefile for:   tinker
+# Version required:    3.6
+# Date Created:                26 August 1998
+# Whom:                        Glenn Johnson
+#
+# $Id$
+#
+
+DISTNAME=      tinker
+PKGNAME=       tinker-3.6
+CATEGORIES=    biology
+MASTER_SITES=  ftp://dasher.wustl.edu/pub/
+
+MAINTAINER=    gjohnson@nola.srrc.usda.gov
+
+LIB_DEPENDS=	U77:${PORTSDIR}/devel/libU77
+
+# If you have EGCS installed you can uncomment the following
+# line and comment out the LIB_DEPENDS line above
+#BUILD_DEPENDS=	g77:${PORTSDIR}/lang/egcs
+
+.include <bsd.port.pre.mk>
+
+WRKSRC=                ${WRKDIR}/tinker/source
+
+MAKEFILE=      ${WRKDIR}/tinker/make/Makefile
+ALL_TARGET=    all listing
+INSTALL_TARGET=        rename
+
+RESTRICTED=    author requests no distribution except from his FTP site
+
+post-install:
+	${MKDIR} ${PREFIX}/share/tinker/params
+	${INSTALL_DATA} ${WRKDIR}/tinker/params/* \
+${PREFIX}/share/tinker/params
+	${INSTALL_DATA} ${WRKDIR}/tinker/source/tinker.txt \
+${PREFIX}/share/tinker
+.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} ${WRKDIR}/tinker/doc/*.ps \
+${PREFIX}/share/tinker/doc
+	${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.Z \
+${PREFIX}/share/tinker/doc
+	${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.txt \
+${PREFIX}/share/tinker/doc
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/README \
+${PREFIX}/share/tinker/example
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/anion.dyn0 \
+${PREFIX}/share/tinker/example
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.in* \
+${PREFIX}/share/tinker/example
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.key \
+${PREFIX}/share/tinker/example
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.log \
+${PREFIX}/share/tinker/example
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.xyz \
+${PREFIX}/share/tinker/example
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/argon.1st \
+${PREFIX}/share/tinker/example
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/crambin.pdb \
+${PREFIX}/share/tinker/example
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/cyclohex.boat \
+${PREFIX}/share/tinker/example
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/cyclohex.chair \
+${PREFIX}/share/tinker/example
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/formamide.cell \
+${PREFIX}/share/tinker/example
+	${INSTALL_SCRIPT} ${WRKDIR}/tinker/example/clean.make \
+${PREFIX}/share/tinker/example
+	${INSTALL_SCRIPT} ${WRKDIR}/tinker/example/*.run \
+${PREFIX}/share/tinker/example
+	${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.input \
+${PREFIX}/share/tinker/bench
+	${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.key \
+${PREFIX}/share/tinker/bench
+	${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.xyz \
+${PREFIX}/share/tinker/bench
+	${INSTALL_DATA} ${WRKDIR}/tinker/bench/water.dyn0 \
+${PREFIX}/share/tinker/bench
+	${INSTALL_DATA} ${WRKDIR}/tinker/bench/results* \
+${PREFIX}/share/tinker/bench
+	${INSTALL_SCRIPT} ${WRKDIR}/tinker/bench/*.run \
+${PREFIX}/share/tinker/bench
+	${INSTALL_DATA} ${WRKDIR}/tinker/test/* ${PREFIX}/share/tinker/test
+.endif
+	@${ECHO} ""
+	@${ECHO} "   **********************************************************"
+	@${ECHO} "       The author requests that you return a license form    "
+	@${ECHO} "          to him if you find Tinker to be useful.            "
+	@${ECHO} "                                                             "
+	@${ECHO} "       See ${PREFIX}/share/tinker/doc for license forms.     "
+	@${ECHO} "   **********************************************************"
+	@${ECHO} ""
+
+.include <bsd.port.post.mk>
diff --git a/biology/tinker/distinfo b/biology/tinker/distinfo
new file mode 100644
index 000000000000..83ef8bd973ed
--- /dev/null
+++ b/biology/tinker/distinfo
@@ -0,0 +1 @@
+MD5 (tinker.tar.gz) = 9b21715ee725eddbcd750a1d0f5836b4
diff --git a/biology/tinker/files/patch-aa b/biology/tinker/files/patch-aa
new file mode 100644
index 000000000000..455841a57a8e
--- /dev/null
+++ b/biology/tinker/files/patch-aa
@@ -0,0 +1,218 @@
+*** ../make/Makefile.orig	Sat Apr 11 11:38:14 1998
+--- ../make/Makefile	Sat Nov 14 02:05:02 1998
+***************
+*** 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 ****
+--- 104,134 ----
+  #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 ${FC}==f77
++ LIBS = -lU77
++ F77FLAGS = -NL400 -c
++ LINKFLAGS = -L${PREFIX}/lib
++ .elseif ${FC}==g77
++ LIBS=
++ F77FLAGS = -Wno-globals -fno-globals -c
++ LINKFLAGS =
++ .endif
++ 
++ OPTFLAGS = ${FFLAGS} -ffast-math -malign-double
++ LIBFLAGS = -rcuv
++ diagq.o:
++ 	${F77} ${F77FLAGS} -ffast-math diagq.f
++ 
+  #################################################################
+  ##  Should not be Necessary to Change Things Below this Point  ##
+  #################################################################
+***************
+*** 766,771 ****
+--- 791,797 ----
+          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
+--- 883,932 ----
+  	${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
diff --git a/biology/tinker/files/patch-ab b/biology/tinker/files/patch-ab
new file mode 100644
index 000000000000..c24301fb8ea3
--- /dev/null
+++ b/biology/tinker/files/patch-ab
@@ -0,0 +1,19 @@
+*** ../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 
diff --git a/biology/tinker/files/patch-ac b/biology/tinker/files/patch-ac
new file mode 100644
index 000000000000..79fbd359856e
--- /dev/null
+++ b/biology/tinker/files/patch-ac
@@ -0,0 +1,13 @@
+*** ../doc/summary.txt.orig    Fri Aug 28 23:50:17 1998
+--- ../doc/summary.txt Fri Aug 28 23:50:33 1998
+***************
+*** 1,4 ****
+!         TINKER ­ Software Tools for Molecular Design
+  
+        Jay Ponder Lab, Dept. of Biochemistry & Molecular 
+                           Biophysics,
+--- 1,4 ----
+!         TINKER -- Software Tools for Molecular Design
+  
+        Jay Ponder Lab, Dept. of Biochemistry & Molecular 
+                           Biophysics,
diff --git a/biology/tinker/files/patch-ad b/biology/tinker/files/patch-ad
new file mode 100644
index 000000000000..7171c8290043
--- /dev/null
+++ b/biology/tinker/files/patch-ad
@@ -0,0 +1,7 @@
+*** ../bench/crambin.run.orig  Sat Aug 29 21:54:06 1998
+--- ../bench/crambin.run       Sat Aug 29 21:54:20 1998
+***************
+*** 1 ****
+! ../bin/timer < crambin.input
+--- 1 ----
+! timer < crambin.input
diff --git a/biology/tinker/files/patch-ae b/biology/tinker/files/patch-ae
new file mode 100644
index 000000000000..d8d1efdaf941
--- /dev/null
+++ b/biology/tinker/files/patch-ae
@@ -0,0 +1,7 @@
+*** ../bench/crystal.run.orig  Sat Aug 29 21:56:20 1998
+--- ../bench/crystal.run       Sat Aug 29 21:56:30 1998
+***************
+*** 1 ****
+! ../bin/timer < crystal.input
+--- 1 ----
+! timer < crystal.input
diff --git a/biology/tinker/files/patch-af b/biology/tinker/files/patch-af
new file mode 100644
index 000000000000..a1fa92a8963a
--- /dev/null
+++ b/biology/tinker/files/patch-af
@@ -0,0 +1,11 @@
+*** ../bench/water.run.orig    Sat Aug 29 21:56:44 1998
+--- ../bench/water.run Sat Aug 29 21:56:58 1998
+***************
+*** 1,3 ****
+  cp water.dyn0 water.dyn
+! time ../bin/dynamic < water.input
+  rm water.dyn
+--- 1,3 ----
+  cp water.dyn0 water.dyn
+! time dynamic < water.input
+  rm water.dyn
diff --git a/biology/tinker/pkg-comment b/biology/tinker/pkg-comment
new file mode 100644
index 000000000000..61cbdec11bb1
--- /dev/null
+++ b/biology/tinker/pkg-comment
@@ -0,0 +1 @@
+a general purpose molecular modelling package.
diff --git a/biology/tinker/pkg-descr b/biology/tinker/pkg-descr
new file mode 100644
index 000000000000..7a3ea6c47453
--- /dev/null
+++ b/biology/tinker/pkg-descr
@@ -0,0 +1,12 @@
+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.
+
+Tinker employs several force fields and minimizaation techniques.
+Simulated annealing and molecular dynamics can be performed with
+Tinker.
+
+For more information visit the web page at:
+
+http://dasher.wustl.edu/tinker/
diff --git a/biology/tinker/pkg-plist b/biology/tinker/pkg-plist
new file mode 100644
index 000000000000..80f3c8486d6d
--- /dev/null
+++ b/biology/tinker/pkg-plist
@@ -0,0 +1,336 @@
+bin/alchemy
+bin/analyze
+bin/anneal
+bin/archive
+bin/correlate
+bin/crystal
+bin/distgeom
+bin/document
+bin/dynamic
+bin/gda
+bin/intedit
+bin/intxyz
+bin/minimize
+bin/minirot
+bin/newton
+bin/newtrot
+bin/optimize
+bin/optirot
+bin/optrigid
+bin/path
+bin/pdbxyz
+bin/protein
+bin/pss
+bin/pssrigid
+bin/pssrot
+bin/saddle
+bin/sniffer
+bin/spacefill
+bin/superpose
+bin/sybylxyz
+bin/testgrad
+bin/testhess
+bin/testlight
+bin/testrot
+bin/timer
+bin/timerot
+bin/vibrate
+bin/vibrot
+bin/xtalfit
+bin/xtalmin
+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/doc/README
+share/tinker/doc/guide.ps.Z
+share/tinker/doc/guide.txt
+share/tinker/doc/license.ps
+share/tinker/doc/license.txt
+share/tinker/doc/logo.ps.Z
+share/tinker/doc/spine.ps
+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
+share/tinker/example/anion.in2
+share/tinker/example/anion.key
+share/tinker/example/anion.log
+share/tinker/example/anion.run
+share/tinker/example/anion.xyz
+share/tinker/example/argon.1st
+share/tinker/example/argon.in1
+share/tinker/example/argon.in2
+share/tinker/example/argon.key
+share/tinker/example/argon.log
+share/tinker/example/argon.run
+share/tinker/example/clean.make
+share/tinker/example/cluster.in1
+share/tinker/example/cluster.key
+share/tinker/example/cluster.log
+share/tinker/example/cluster.run
+share/tinker/example/cluster.xyz
+share/tinker/example/crambin.in1
+share/tinker/example/crambin.in2
+share/tinker/example/crambin.in3
+share/tinker/example/crambin.key
+share/tinker/example/crambin.log
+share/tinker/example/crambin.pdb
+share/tinker/example/crambin.run
+share/tinker/example/cyclohex.boat
+share/tinker/example/cyclohex.chair
+share/tinker/example/cyclohex.in1
+share/tinker/example/cyclohex.in2
+share/tinker/example/cyclohex.in3
+share/tinker/example/cyclohex.key
+share/tinker/example/cyclohex.log
+share/tinker/example/cyclohex.run
+share/tinker/example/enkephalin.in1
+share/tinker/example/enkephalin.in2
+share/tinker/example/enkephalin.in3
+share/tinker/example/enkephalin.key
+share/tinker/example/enkephalin.log
+share/tinker/example/enkephalin.run
+share/tinker/example/formamide.cell
+share/tinker/example/formamide.in1
+share/tinker/example/formamide.in2
+share/tinker/example/formamide.in3
+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/test/README
+share/tinker/test/ala20.key
+share/tinker/test/ala20.xyz
+share/tinker/test/annulene.int
+share/tinker/test/annulene.key
+share/tinker/test/annulene.xyz
+share/tinker/test/annulene2.key
+share/tinker/test/annulene2.xyz
+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/benzene.int
+share/tinker/test/benzene.key
+share/tinker/test/benzene.xyz
+share/tinker/test/butane.int
+share/tinker/test/butane.key
+share/tinker/test/butane.xyz
+share/tinker/test/butane2.int
+share/tinker/test/butane2.key
+share/tinker/test/butane2.xyz
+share/tinker/test/butanes.dyn
+share/tinker/test/butanes.key
+share/tinker/test/butanes.xyz
+share/tinker/test/butanex.key
+share/tinker/test/butanex.xyz
+share/tinker/test/butopls.int
+share/tinker/test/butopls.key
+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.xyz
+share/tinker/test/c7ax.int
+share/tinker/test/c7ax.key
+share/tinker/test/c7ax.xyz
+share/tinker/test/c7eq.int
+share/tinker/test/c7eq.key
+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.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.xyz
+share/tinker/test/cyclo.int
+share/tinker/test/cyclo.key
+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.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.seq
+share/tinker/test/enkephalin.xyz
+share/tinker/test/ermer.int
+share/tinker/test/ermer.key
+share/tinker/test/ermer.xyz
+share/tinker/test/ethane.int
+share/tinker/test/ethane.key
+share/tinker/test/ethane.xyz
+share/tinker/test/ethylene.int
+share/tinker/test/ethylene.key
+share/tinker/test/ethylene.xyz
+share/tinker/test/flane.int
+share/tinker/test/flane.key
+share/tinker/test/flane.xyz
+share/tinker/test/furan.int
+share/tinker/test/furan.key
+share/tinker/test/furan.xyz
+share/tinker/test/glucose.key
+share/tinker/test/glucose.xyz
+share/tinker/test/helix.key
+share/tinker/test/helix.xyz
+share/tinker/test/imidazole.int
+share/tinker/test/imidazole.key
+share/tinker/test/imidazole.xyz
+share/tinker/test/imine.int
+share/tinker/test/imine.key
+share/tinker/test/imine.xyz
+share/tinker/test/lactam.key
+share/tinker/test/lactam.xyz
+share/tinker/test/methane.int
+share/tinker/test/methane.key
+share/tinker/test/methane.xyz
+share/tinker/test/methanol.key
+share/tinker/test/methanol.xyz
+share/tinker/test/nma.key
+share/tinker/test/nma.xyz
+share/tinker/test/nmabox.dyn
+share/tinker/test/nmabox.key
+share/tinker/test/nmabox.xyz
+share/tinker/test/nstilbene.int
+share/tinker/test/nstilbene.key
+share/tinker/test/nstilbene.xyz
+share/tinker/test/octane.int
+share/tinker/test/octane.key
+share/tinker/test/octane.xyz
+share/tinker/test/octane2.int
+share/tinker/test/octane2.key
+share/tinker/test/octane2.xyz
+share/tinker/test/octene.key
+share/tinker/test/octene.xyz
+share/tinker/test/palmitate.key
+share/tinker/test/palmitate.xyz
+share/tinker/test/peptide.int
+share/tinker/test/peptide.key
+share/tinker/test/peptide.make
+share/tinker/test/peptide.pdb
+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
+share/tinker/test/pyridine.int
+share/tinker/test/pyridine.key
+share/tinker/test/pyridine.xyz
+share/tinker/test/pyrrole.int
+share/tinker/test/pyrrole.key
+share/tinker/test/pyrrole.xyz
+share/tinker/test/retinoic.key
+share/tinker/test/retinoic.xyz
+share/tinker/test/sterol.key
+share/tinker/test/sterol.xyz
+share/tinker/test/styrene.int
+share/tinker/test/styrene.key
+share/tinker/test/styrene.xyz
+share/tinker/test/thiadiene.int
+share/tinker/test/thiadiene.key
+share/tinker/test/thiadiene.xyz
+share/tinker/test/thiophene.int
+share/tinker/test/thiophene.key
+share/tinker/test/thiophene.xyz
+share/tinker/test/thr.int
+share/tinker/test/thr.key
+share/tinker/test/thr.xyz
+share/tinker/test/water.int
+share/tinker/test/water.key
+share/tinker/test/water.xyz
+share/tinker/test/waterbig.key
+share/tinker/test/waterbig.xyz
+share/tinker/test/waterbox.dyn
+share/tinker/test/waterbox.key
+share/tinker/test/waterbox.xyz
+share/tinker/test/waterhuge.key
+share/tinker/test/waterhuge.xyz
+share/tinker/test/wateroct.dyn
+share/tinker/test/wateroct.key
+share/tinker/test/wateroct.xyz
+share/tinker/test/watersmall.dyn
+share/tinker/test/watersmall.key
+share/tinker/test/watersmall.xyz
+share/tinker/test/white.int
+share/tinker/test/white.key
+share/tinker/test/white.xyz
+@dirrm share/tinker/params
+@dirrm share/tinker/doc
+@dirrm share/tinker/example
+@dirrm share/tinker/bench
+@dirrm share/tinker/test
+@dirrm share/tinker