Update tinker from version 3.6 to version 3.7

PR:	12301
Submitted by:	maintainer

7 files changed, 289 insertions, 310 deletions

diff --git a/biology/tinker/Makefile b/biology/tinker/Makefile
index b4161f6fcbda..5f7062ba7a07 100644
--- a/biology/tinker/Makefile
+++ b/biology/tinker/Makefile
@@ -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
@@ -35,11 +38,12 @@ 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
@@ -47,6 +51,8 @@ ${PREFIX}/share/tinker
 	${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
 	${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.Z \
@@ -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} "   **********************************************************"
diff --git a/biology/tinker/distinfo b/biology/tinker/distinfo
index 83ef8bd973ed..067476a5dba7 100644
--- a/biology/tinker/distinfo
+++ b/biology/tinker/distinfo
@@ -1 +1 @@
-MD5 (tinker.tar.gz) = 9b21715ee725eddbcd750a1d0f5836b4
+MD5 (tinker.tar.gz) = 1b05697908aecb88aee9054188f8ac7f
diff --git a/biology/tinker/files/patch-aa b/biology/tinker/files/patch-aa
index fecd6d99f52c..aa842b867c34 100644
--- a/biology/tinker/files/patch-aa
+++ b/biology/tinker/files/patch-aa
@@ -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
diff --git a/biology/tinker/files/patch-ab b/biology/tinker/files/patch-ab
index c24301fb8ea3..5fbcd518580c 100644
--- a/biology/tinker/files/patch-ab
+++ b/biology/tinker/files/patch-ab
@@ -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 
diff --git a/biology/tinker/files/patch-ac b/biology/tinker/files/patch-ac
index 79fbd359856e..e21d420dce16 100644
--- a/biology/tinker/files/patch-ac
+++ b/biology/tinker/files/patch-ac
@@ -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,
diff --git a/biology/tinker/pkg-descr b/biology/tinker/pkg-descr
index c450dda1b85f..eee99649421d 100644
--- a/biology/tinker/pkg-descr
+++ b/biology/tinker/pkg-descr
@@ -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/
diff --git a/biology/tinker/pkg-plist b/biology/tinker/pkg-plist
index 80f3c8486d6d..63f55046e0dc 100644
--- a/biology/tinker/pkg-plist
+++ b/biology/tinker/pkg-plist
@@ -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