Update to 3.9

PR:		30398
Submitted by:	MAINTAINER

12 files changed, 161 insertions, 116 deletions

diff --git a/biology/tinker/Makefile b/biology/tinker/Makefile
index 98cf283d0b09..8430abc675ae 100644
--- a/biology/tinker/Makefile
+++ b/biology/tinker/Makefile
@@ -6,8 +6,7 @@
 #
 
 PORTNAME=	tinker
-PORTVERSION=	3.8
-PORTREVISION=	1
+PORTVERSION=	3.9
 CATEGORIES=	biology
 MASTER_SITES=	ftp://dasher.wustl.edu/pub/
 DISTNAME=	${PORTNAME}
@@ -24,6 +23,11 @@ INSTALL_TARGET=	rename
 
 RESTRICTED=	author requests no distribution except from his FTP site
 
+pre-fetch:
+	@${ECHO_MSG} ""
+	@${ECHO_MSG} If you get a CHECKSUM mismatch, try doing a \'make distclean\' first.
+	@${ECHO_MSG} ""
+
 .if defined(WANT_VIEWER)
 .if ${XFREE86_VERSION} == 3
 BUILD_DEPENDS+=	imake:${PORTSDIR}/devel/imake
@@ -65,8 +69,12 @@ ${PREFIX}/share/doc/tinker
 ${PREFIX}/share/doc/tinker
 	${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.txt \
 ${PREFIX}/share/doc/tinker
+	${INSTALL_DATA} ${WRKDIR}/tinker/doc/release* \
+${PREFIX}/share/doc/tinker
 	${INSTALL_DATA} ${WRKDIR}/tinker/example/README \
 ${PREFIX}/share/examples/tinker
+	${INSTALL_SCRIPT} ${WRKDIR}/tinker/example/clean.make \
+${PREFIX}/share/examples/tinker
 	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.1st \
 ${PREFIX}/share/examples/tinker
 	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.boat \
@@ -87,29 +95,31 @@ ${PREFIX}/share/examples/tinker
 ${PREFIX}/share/examples/tinker
 	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.xyz \
 ${PREFIX}/share/examples/tinker
-	${INSTALL_SCRIPT} ${WRKDIR}/tinker/example/clean.make \
-${PREFIX}/share/examples/tinker
 	${INSTALL_SCRIPT} ${WRKDIR}/tinker/example/*.run \
 ${PREFIX}/share/examples/tinker
+	${INSTALL_DATA} ${WRKDIR}/tinker/bench/README \
+${PREFIX}/share/tinker/bench
 	${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.dyn0 \
 ${PREFIX}/share/tinker/bench
 	${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.log \
 ${PREFIX}/share/tinker/bench
 	${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.key \
 ${PREFIX}/share/tinker/bench
+	${INSTALL_SCRIPT} ${WRKDIR}/tinker/bench/*.run \
+${PREFIX}/share/tinker/bench
 	${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.xyz \
 ${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
 
 .if defined(WANT_VIEWER)
 	${MKDIR} ${PREFIX}/share/tinker/rasmol
 	${INSTALL_PROGRAM} ${WRKDIR}/tinker/rasmol/tview-* ${PREFIX}/bin
-	${INSTALL_DATA} ${WRKDIR}/tinker/rasmol/rasmol.hlp ${PREFIX}/share/tinker/rasmol
+	${INSTALL_SCRIPT} ${FILESDIR}/tview ${PREFIX}/bin
+	${INSTALL_DATA} ${WRKDIR}/tinker/rasmol/rasmol.hlp \
+		${PREFIX}/share/tinker/rasmol
 
 .endif
 
diff --git a/biology/tinker/distinfo b/biology/tinker/distinfo
index a22df5355677..3d11520fdd4f 100644
--- a/biology/tinker/distinfo
+++ b/biology/tinker/distinfo
@@ -1 +1 @@
-MD5 (tinker.tar.gz) = 11e66fb5452e2153a2ced410ea9acadb
+MD5 (tinker.tar.gz) = a48fc15fe668f8e41d0cc3316a582928
diff --git a/biology/tinker/files/patch-aa b/biology/tinker/files/patch-aa
index c12a46cb6f62..e9cf0c948aaf 100644
--- a/biology/tinker/files/patch-aa
+++ b/biology/tinker/files/patch-aa
@@ -1,5 +1,5 @@
---- ../make/Makefile.orig	Mon Jan 15 12:39:52 2001
-+++ ../make/Makefile	Thu Apr 19 14:39:26 2001
+--- ../make/Makefile.orig	Sat Jul 21 10:04:48 2001
++++ ../make/Makefile	Wed Sep  5 13:51:19 2001
 @@ -9,8 +9,8 @@
  ##
  ##   1. make all              Build all the TINKER executables
@@ -68,7 +68,7 @@
  #################################################################
  ##  Should not be Necessary to Change Things Below this Point  ##
  #################################################################
-@@ -486,11 +504,13 @@
+@@ -494,11 +512,13 @@
             xyzpdb.x \
             xyzsybyl.x
  
@@ -84,7 +84,7 @@
  
  all:	${EXEFILES}
  
-@@ -501,56 +521,56 @@
+@@ -509,57 +529,57 @@
  	cat *.i *.f > tinker.txt
  
  rename:
@@ -112,6 +112,7 @@
 -	mv  optrigid.x   $(BINDIR)/optrigid
 -	mv  path.x       $(BINDIR)/path
 -	mv  pdbxyz.x     $(BINDIR)/pdbxyz
+-	mv  polarize.x   $(BINDIR)/polarize
 -	mv  protein.x    $(BINDIR)/protein
 -	mv  pss.x        $(BINDIR)/pss
 -	mv  pssrigid.x   $(BINDIR)/pssrigid
@@ -162,6 +163,7 @@
 +	${INSTALL_PROGRAM}  optrigid.x   $(BINDIR)/optrigid
 +	${INSTALL_PROGRAM}  path.x       $(BINDIR)/path
 +	${INSTALL_PROGRAM}  pdbxyz.x     $(BINDIR)/pdbxyz
++	${INSTALL_PROGRAM}  polarize.x   $(BINDIR)/polarize
 +	${INSTALL_PROGRAM}  protein.x    $(BINDIR)/protein
 +	${INSTALL_PROGRAM}  pss.x        $(BINDIR)/pss
 +	${INSTALL_PROGRAM}  pssrigid.x   $(BINDIR)/pssrigid
@@ -191,7 +193,7 @@
  
  remove_links:
  	rm -f $(LINKDIR)/alchemy
-@@ -671,8 +691,8 @@
+@@ -682,8 +702,8 @@
          bspline.o \
          calendar.o \
          center.o \
diff --git a/biology/tinker/files/patch-ag b/biology/tinker/files/patch-ag
deleted file mode 100644
index a1084876fe7d..000000000000
--- a/biology/tinker/files/patch-ag
+++ /dev/null
@@ -1,11 +0,0 @@
---- sizes.i.orig	Fri Jan 12 11:43:06 2001
-+++ sizes.i	Fri Jan 12 11:43:38 2001
-@@ -52,7 +52,7 @@
-       integer maxvar,maxopt,maxhess,maxlight,maxvib,maxgeo,maxcell
-       integer maxring,maxfix,maxbio,maxres,maxamino,maxnuc,maxbnd
-       integer maxang,maxtors,maxpi,maxpib,maxpit
--      parameter (maxatm=10000)
-+      parameter (maxatm=2500)
-       parameter (maxval=4)
-       parameter (maxgrp=100)
-       parameter (maxtyp=1000)
diff --git a/biology/tinker/files/patch-ah b/biology/tinker/files/patch-ah
index c3f23dd2e057..12bd7c9ac00d 100644
--- a/biology/tinker/files/patch-ah
+++ b/biology/tinker/files/patch-ah
@@ -1,5 +1,5 @@
---- ../bench/bench-1.run.orig	Tue Jan  9 14:28:53 2001
-+++ ../bench/bench-1.run	Tue Jan  9 14:29:19 2001
+--- ../bench/bench1.run.orig	Tue Jul 24 14:02:20 2001
++++ ../bench/bench1.run	Wed Sep  5 13:57:02 2001
 @@ -1 +1 @@
--../bin/timer bench-1 1 y
-+timer bench-1 1 y
+-../bin/timer bench1 1 y
++timer bench1 1 y
diff --git a/biology/tinker/files/patch-ai b/biology/tinker/files/patch-ai
index 643cc82de1ed..e5a6559bb29f 100644
--- a/biology/tinker/files/patch-ai
+++ b/biology/tinker/files/patch-ai
@@ -1,5 +1,5 @@
---- ../bench/bench-2.run.orig	Tue Jan  9 14:29:26 2001
-+++ ../bench/bench-2.run	Tue Jan  9 14:29:33 2001
+--- ../bench/bench2.run.orig	Tue Jul 24 14:02:20 2001
++++ ../bench/bench2.run	Wed Sep  5 13:58:47 2001
 @@ -1 +1 @@
--../bin/timer bench-2 1 y
-+timer bench-2 1 y
+-../bin/timer bench2 1 y
++timer bench2 1 y
diff --git a/biology/tinker/files/patch-aj b/biology/tinker/files/patch-aj
index 1f36c30fe172..3e18d09b5071 100644
--- a/biology/tinker/files/patch-aj
+++ b/biology/tinker/files/patch-aj
@@ -1,5 +1,5 @@
---- ../bench/bench-3.run.orig	Tue Jan  9 14:29:40 2001
-+++ ../bench/bench-3.run	Tue Jan  9 14:29:53 2001
+--- ../bench/bench3.run.orig	Wed Sep  5 14:00:09 2001
++++ ../bench/bench3.run	Wed Sep  5 14:01:27 2001
 @@ -1 +1 @@
--time ../bin/vibrate bench-3 0
-+time vibrate bench-3 0
+-time ../bin/vibrate bench3 0
++time vibrate bench3 0
diff --git a/biology/tinker/files/patch-ak b/biology/tinker/files/patch-ak
index d0549d42829d..9a415fcd0f32 100644
--- a/biology/tinker/files/patch-ak
+++ b/biology/tinker/files/patch-ak
@@ -1,7 +1,7 @@
---- ../bench/bench-4.run.orig	Tue Jan  9 14:29:59 2001
-+++ ../bench/bench-4.run	Tue Jan  9 14:30:14 2001
+--- ../bench/bench4.run.orig	Tue Jul 24 14:02:20 2001
++++ ../bench/bench4.run	Wed Sep  5 14:02:17 2001
 @@ -1,3 +1,3 @@
- cp bench-4.dyn0 bench-4.dyn
--time ../bin/dynamic bench-4 1000 1.0 10.0 2 298.0
-+time dynamic bench-4 1000 1.0 10.0 2 298.0
- rm bench-4.dyn
+ cp bench4.dyn0 bench4.dyn
+-time ../bin/dynamic bench4 1000 1.0 10.0 2 298.0
++time dynamic bench4 1000 1.0 10.0 2 298.0
+ rm bench4.dyn
diff --git a/biology/tinker/files/patch-al b/biology/tinker/files/patch-al
index 8127254d2daa..e85fd419c12f 100644
--- a/biology/tinker/files/patch-al
+++ b/biology/tinker/files/patch-al
@@ -1,7 +1,7 @@
---- ../bench/bench-5.run.orig	Tue Jan  9 14:30:18 2001
-+++ ../bench/bench-5.run	Tue Jan  9 14:30:29 2001
+--- ../bench/bench5.run.orig	Tue Jul 24 14:02:20 2001
++++ ../bench/bench5.run	Wed Sep  5 14:03:07 2001
 @@ -1,3 +1,3 @@
- cp bench-5.dyn0 bench-5.dyn
--time ../bin/dynamic bench-5 100 1.0 10.0 2 298.0
-+time dynamic bench-5 100 1.0 10.0 2 298.0
- rm bench-5.dyn
+ cp bench5.dyn0 bench5.dyn
+-time ../bin/dynamic bench5 100 1.0 10.0 2 298.0
++time dynamic bench5 100 1.0 10.0 2 298.0
+ rm bench5.dyn
diff --git a/biology/tinker/files/tview b/biology/tinker/files/tview
new file mode 100644
index 000000000000..834dd72ba166
--- /dev/null
+++ b/biology/tinker/files/tview
@@ -0,0 +1,21 @@
+#!/bin/sh
+
+# Determine if X is running
+if [ -z $DISPLAY ]; then
+	echo You must be running X for this.
+else
+# Try to determine the color depth of the X server
+
+	DEPTH=`xwininfo -root | grep Depth | awk '{print $2}'`
+
+	if [ $DEPTH = 24 -o $DEPTH = 32 ]; then
+		PROGRAM=tview-32
+	elif [ $DEPTH = 16 ]; then
+		PROGRAM=tview-16
+	elif [ $DEPTH = 8 ]; then
+		PROGRAM=tview-8
+	else
+		echo Can not determine color depth of Display $DISPLAY
+	fi
+	exec $PROGRAM $@
+fi
diff --git a/biology/tinker/pkg-plist b/biology/tinker/pkg-plist
index afba39f57dc1..fab9edbff2ef 100644
--- a/biology/tinker/pkg-plist
+++ b/biology/tinker/pkg-plist
@@ -22,6 +22,7 @@ bin/optirot
 bin/optrigid
 bin/path
 bin/pdbxyz
+bin/polarize
 bin/protein
 bin/pss
 bin/pssrigid
@@ -49,7 +50,6 @@ bin/xyzint
 bin/xyzpdb
 bin/xyzsybyl
 %%PORTDOCS%%share/doc/tinker/README
-%%PORTDOCS%%share/doc/tinker/announce.txt
 %%PORTDOCS%%share/doc/tinker/guide.pdf
 %%PORTDOCS%%share/doc/tinker/guide.ps.gz
 %%PORTDOCS%%share/doc/tinker/guide.txt
@@ -58,6 +58,11 @@ bin/xyzsybyl
 %%PORTDOCS%%share/doc/tinker/license.txt
 %%PORTDOCS%%share/doc/tinker/logo.pdf
 %%PORTDOCS%%share/doc/tinker/logo.ps.gz
+%%PORTDOCS%%share/doc/tinker/release-3.2
+%%PORTDOCS%%share/doc/tinker/release-3.6
+%%PORTDOCS%%share/doc/tinker/release-3.7
+%%PORTDOCS%%share/doc/tinker/release-3.8
+%%PORTDOCS%%share/doc/tinker/release-3.9
 %%PORTDOCS%%share/doc/tinker/summary.pdf
 %%PORTDOCS%%share/doc/tinker/summary.ps
 %%PORTDOCS%%share/doc/tinker/summary.txt
@@ -104,24 +109,26 @@ bin/xyzsybyl
 %%PORTDOCS%%share/examples/tinker/salt.key
 %%PORTDOCS%%share/examples/tinker/salt.log
 %%PORTDOCS%%share/examples/tinker/salt.run
-%%PORTDOCS%%share/tinker/bench/bench-1.key
-%%PORTDOCS%%share/tinker/bench/bench-1.run
-%%PORTDOCS%%share/tinker/bench/bench-1.xyz
-%%PORTDOCS%%share/tinker/bench/bench-2.key
-%%PORTDOCS%%share/tinker/bench/bench-2.run
-%%PORTDOCS%%share/tinker/bench/bench-2.xyz
-%%PORTDOCS%%share/tinker/bench/bench-3.key
-%%PORTDOCS%%share/tinker/bench/bench-3.run
-%%PORTDOCS%%share/tinker/bench/bench-3.xyz
-%%PORTDOCS%%share/tinker/bench/bench-4.dyn0
-%%PORTDOCS%%share/tinker/bench/bench-4.key
-%%PORTDOCS%%share/tinker/bench/bench-4.log
-%%PORTDOCS%%share/tinker/bench/bench-4.run
-%%PORTDOCS%%share/tinker/bench/bench-4.xyz
-%%PORTDOCS%%share/tinker/bench/bench-5.dyn0
-%%PORTDOCS%%share/tinker/bench/bench-5.key
-%%PORTDOCS%%share/tinker/bench/bench-5.run
-%%PORTDOCS%%share/tinker/bench/bench-5.xyz
+%%PORTDOCS%%share/tinker/bench/README
+%%PORTDOCS%%share/tinker/bench/bench1.key
+%%PORTDOCS%%share/tinker/bench/bench1.run
+%%PORTDOCS%%share/tinker/bench/bench1.xyz
+%%PORTDOCS%%share/tinker/bench/bench2.key
+%%PORTDOCS%%share/tinker/bench/bench2.run
+%%PORTDOCS%%share/tinker/bench/bench2.xyz
+%%PORTDOCS%%share/tinker/bench/bench3.key
+%%PORTDOCS%%share/tinker/bench/bench3.run
+%%PORTDOCS%%share/tinker/bench/bench3.xyz
+%%PORTDOCS%%share/tinker/bench/bench4.dyn0
+%%PORTDOCS%%share/tinker/bench/bench4.key
+%%PORTDOCS%%share/tinker/bench/bench4.log
+%%PORTDOCS%%share/tinker/bench/bench4.run
+%%PORTDOCS%%share/tinker/bench/bench4.xyz
+%%PORTDOCS%%share/tinker/bench/bench5.dyn0
+%%PORTDOCS%%share/tinker/bench/bench5.key
+%%PORTDOCS%%share/tinker/bench/bench5.log
+%%PORTDOCS%%share/tinker/bench/bench5.run
+%%PORTDOCS%%share/tinker/bench/bench5.xyz
 %%PORTDOCS%%share/tinker/bench/results-2.3
 %%PORTDOCS%%share/tinker/bench/results-2.4
 %%PORTDOCS%%share/tinker/bench/results-2.9
@@ -131,11 +138,11 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/bench/results-3.5
 %%PORTDOCS%%share/tinker/bench/results-3.7
 %%PORTDOCS%%share/tinker/bench/results-3.8
+%%PORTDOCS%%share/tinker/bench/results-3.9
 %%PORTDOCS%%share/tinker/params/README
 %%PORTDOCS%%share/tinker/params/amber.prm
-%%PORTDOCS%%share/tinker/params/amberN.prm
 %%PORTDOCS%%share/tinker/params/charmm.prm
-%%PORTDOCS%%share/tinker/params/emr.prm
+%%PORTDOCS%%share/tinker/params/dudek.prm
 %%PORTDOCS%%share/tinker/params/hoch.prm
 %%PORTDOCS%%share/tinker/params/mm2.prm
 %%PORTDOCS%%share/tinker/params/mm3.prm
@@ -144,7 +151,6 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/params/oplsaa.prm
 %%PORTDOCS%%share/tinker/params/smooth.prm
 %%PORTDOCS%%share/tinker/params/smoothaa.prm
-%%PORTDOCS%%share/tinker/params/tinker.prm
 %%PORTDOCS%%share/tinker/params/water.prm
 %%PORTDOCS%%share/tinker/test/README
 %%PORTDOCS%%share/tinker/test/ala20.key
@@ -163,10 +169,8 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/bdna.seq
 %%PORTDOCS%%share/tinker/test/bdna.xyz
 %%PORTDOCS%%share/tinker/test/bearing.key
-%%PORTDOCS%%share/tinker/test/bearing.pdb
 %%PORTDOCS%%share/tinker/test/bearing.xyz
 %%PORTDOCS%%share/tinker/test/bearing2.key
-%%PORTDOCS%%share/tinker/test/bearing2.pdb
 %%PORTDOCS%%share/tinker/test/bearing2.xyz
 %%PORTDOCS%%share/tinker/test/benzene.int
 %%PORTDOCS%%share/tinker/test/benzene.key
@@ -208,10 +212,11 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/calmodulin.pdb
 %%PORTDOCS%%share/tinker/test/calmodulin.seq
 %%PORTDOCS%%share/tinker/test/calmodulin.xyz
+%%PORTDOCS%%share/tinker/test/copper.key
+%%PORTDOCS%%share/tinker/test/copper.xyz
 %%PORTDOCS%%share/tinker/test/cpentene.key
 %%PORTDOCS%%share/tinker/test/cpentene.xyz
 %%PORTDOCS%%share/tinker/test/crambin.key
-%%PORTDOCS%%share/tinker/test/crambin.min
 %%PORTDOCS%%share/tinker/test/crambin.pdb
 %%PORTDOCS%%share/tinker/test/crambin.seq
 %%PORTDOCS%%share/tinker/test/crambin.super
@@ -231,15 +236,15 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/cyclo2.int
 %%PORTDOCS%%share/tinker/test/cyclo2.key
 %%PORTDOCS%%share/tinker/test/cyclo2.xyz
+%%PORTDOCS%%share/tinker/test/dang.key
+%%PORTDOCS%%share/tinker/test/dang.xyz
+%%PORTDOCS%%share/tinker/test/diamond.key
+%%PORTDOCS%%share/tinker/test/diamond.xyz
 %%PORTDOCS%%share/tinker/test/diene.int
 %%PORTDOCS%%share/tinker/test/diene.key
 %%PORTDOCS%%share/tinker/test/diene.xyz
 %%PORTDOCS%%share/tinker/test/dimethane.key
 %%PORTDOCS%%share/tinker/test/dimethane.xyz
-%%PORTDOCS%%share/tinker/test/diwater.key
-%%PORTDOCS%%share/tinker/test/diwater.lin
-%%PORTDOCS%%share/tinker/test/diwater.min
-%%PORTDOCS%%share/tinker/test/diwater.xyz
 %%PORTDOCS%%share/tinker/test/enkephalin.int
 %%PORTDOCS%%share/tinker/test/enkephalin.key
 %%PORTDOCS%%share/tinker/test/enkephalin.make
@@ -273,8 +278,13 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/furan.xyz
 %%PORTDOCS%%share/tinker/test/glucose.key
 %%PORTDOCS%%share/tinker/test/glucose.xyz
+%%PORTDOCS%%share/tinker/test/graphite.key
+%%PORTDOCS%%share/tinker/test/graphite.xyz
+%%PORTDOCS%%share/tinker/test/helix.dyn
 %%PORTDOCS%%share/tinker/test/helix.key
 %%PORTDOCS%%share/tinker/test/helix.xyz
+%%PORTDOCS%%share/tinker/test/heme.key
+%%PORTDOCS%%share/tinker/test/heme.xyz
 %%PORTDOCS%%share/tinker/test/hexane.int
 %%PORTDOCS%%share/tinker/test/hexane.key
 %%PORTDOCS%%share/tinker/test/hexane.xyz
@@ -301,6 +311,7 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/methanol.xyz
 %%PORTDOCS%%share/tinker/test/nacl.key
 %%PORTDOCS%%share/tinker/test/nacl.xyz
+%%PORTDOCS%%share/tinker/test/naphthalene.int
 %%PORTDOCS%%share/tinker/test/naphthalene.key
 %%PORTDOCS%%share/tinker/test/naphthalene.xyz
 %%PORTDOCS%%share/tinker/test/nma.int
@@ -320,21 +331,17 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/octane2.xyz
 %%PORTDOCS%%share/tinker/test/octene.key
 %%PORTDOCS%%share/tinker/test/octene.xyz
+%%PORTDOCS%%share/tinker/test/palmitate.int
 %%PORTDOCS%%share/tinker/test/palmitate.key
 %%PORTDOCS%%share/tinker/test/palmitate.xyz
 %%PORTDOCS%%share/tinker/test/peptide.int
 %%PORTDOCS%%share/tinker/test/peptide.key
 %%PORTDOCS%%share/tinker/test/peptide.make
-%%PORTDOCS%%share/tinker/test/peptide.min
 %%PORTDOCS%%share/tinker/test/peptide.pdb
 %%PORTDOCS%%share/tinker/test/peptide.seq
 %%PORTDOCS%%share/tinker/test/peptide.xyz
 %%PORTDOCS%%share/tinker/test/phenanth.key
 %%PORTDOCS%%share/tinker/test/phenanth.xyz
-%%PORTDOCS%%share/tinker/test/photo.key
-%%PORTDOCS%%share/tinker/test/photo.pdb
-%%PORTDOCS%%share/tinker/test/photo.seq
-%%PORTDOCS%%share/tinker/test/photo.xyz
 %%PORTDOCS%%share/tinker/test/propane.key
 %%PORTDOCS%%share/tinker/test/propane.ray
 %%PORTDOCS%%share/tinker/test/propane.xyz
@@ -365,6 +372,10 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/thr.int
 %%PORTDOCS%%share/tinker/test/thr.key
 %%PORTDOCS%%share/tinker/test/thr.xyz
+%%PORTDOCS%%share/tinker/test/tip3p.key
+%%PORTDOCS%%share/tinker/test/tip3p.xyz
+%%PORTDOCS%%share/tinker/test/tip4p.key
+%%PORTDOCS%%share/tinker/test/tip4p.xyz
 %%PORTDOCS%%share/tinker/test/tip5p.key
 %%PORTDOCS%%share/tinker/test/tip5p.xyz
 %%PORTDOCS%%share/tinker/test/water.int
diff --git a/biology/tinker/pkg-plist.viewer b/biology/tinker/pkg-plist.viewer
index d1d741483e17..851a2eccc975 100644
--- a/biology/tinker/pkg-plist.viewer
+++ b/biology/tinker/pkg-plist.viewer
@@ -22,6 +22,7 @@ bin/optirot
 bin/optrigid
 bin/path
 bin/pdbxyz
+bin/polarize
 bin/protein
 bin/pss
 bin/pssrigid
@@ -40,6 +41,7 @@ bin/testlight
 bin/testrot
 bin/timer
 bin/timerot
+bin/tview
 bin/tview-8
 bin/tview-16
 bin/tview-32
@@ -52,7 +54,6 @@ bin/xyzint
 bin/xyzpdb
 bin/xyzsybyl
 %%PORTDOCS%%share/doc/tinker/README
-%%PORTDOCS%%share/doc/tinker/announce.txt
 %%PORTDOCS%%share/doc/tinker/guide.pdf
 %%PORTDOCS%%share/doc/tinker/guide.ps.gz
 %%PORTDOCS%%share/doc/tinker/guide.txt
@@ -61,6 +62,11 @@ bin/xyzsybyl
 %%PORTDOCS%%share/doc/tinker/license.txt
 %%PORTDOCS%%share/doc/tinker/logo.pdf
 %%PORTDOCS%%share/doc/tinker/logo.ps.gz
+%%PORTDOCS%%share/doc/tinker/release-3.2
+%%PORTDOCS%%share/doc/tinker/release-3.6
+%%PORTDOCS%%share/doc/tinker/release-3.7
+%%PORTDOCS%%share/doc/tinker/release-3.8
+%%PORTDOCS%%share/doc/tinker/release-3.9
 %%PORTDOCS%%share/doc/tinker/summary.pdf
 %%PORTDOCS%%share/doc/tinker/summary.ps
 %%PORTDOCS%%share/doc/tinker/summary.txt
@@ -107,24 +113,26 @@ bin/xyzsybyl
 %%PORTDOCS%%share/examples/tinker/salt.key
 %%PORTDOCS%%share/examples/tinker/salt.log
 %%PORTDOCS%%share/examples/tinker/salt.run
-%%PORTDOCS%%share/tinker/bench/bench-1.key
-%%PORTDOCS%%share/tinker/bench/bench-1.run
-%%PORTDOCS%%share/tinker/bench/bench-1.xyz
-%%PORTDOCS%%share/tinker/bench/bench-2.key
-%%PORTDOCS%%share/tinker/bench/bench-2.run
-%%PORTDOCS%%share/tinker/bench/bench-2.xyz
-%%PORTDOCS%%share/tinker/bench/bench-3.key
-%%PORTDOCS%%share/tinker/bench/bench-3.run
-%%PORTDOCS%%share/tinker/bench/bench-3.xyz
-%%PORTDOCS%%share/tinker/bench/bench-4.dyn0
-%%PORTDOCS%%share/tinker/bench/bench-4.key
-%%PORTDOCS%%share/tinker/bench/bench-4.log
-%%PORTDOCS%%share/tinker/bench/bench-4.run
-%%PORTDOCS%%share/tinker/bench/bench-4.xyz
-%%PORTDOCS%%share/tinker/bench/bench-5.dyn0
-%%PORTDOCS%%share/tinker/bench/bench-5.key
-%%PORTDOCS%%share/tinker/bench/bench-5.run
-%%PORTDOCS%%share/tinker/bench/bench-5.xyz
+%%PORTDOCS%%share/tinker/bench/README
+%%PORTDOCS%%share/tinker/bench/bench1.key
+%%PORTDOCS%%share/tinker/bench/bench1.run
+%%PORTDOCS%%share/tinker/bench/bench1.xyz
+%%PORTDOCS%%share/tinker/bench/bench2.key
+%%PORTDOCS%%share/tinker/bench/bench2.run
+%%PORTDOCS%%share/tinker/bench/bench2.xyz
+%%PORTDOCS%%share/tinker/bench/bench3.key
+%%PORTDOCS%%share/tinker/bench/bench3.run
+%%PORTDOCS%%share/tinker/bench/bench3.xyz
+%%PORTDOCS%%share/tinker/bench/bench4.dyn0
+%%PORTDOCS%%share/tinker/bench/bench4.key
+%%PORTDOCS%%share/tinker/bench/bench4.log
+%%PORTDOCS%%share/tinker/bench/bench4.run
+%%PORTDOCS%%share/tinker/bench/bench4.xyz
+%%PORTDOCS%%share/tinker/bench/bench5.dyn0
+%%PORTDOCS%%share/tinker/bench/bench5.key
+%%PORTDOCS%%share/tinker/bench/bench5.log
+%%PORTDOCS%%share/tinker/bench/bench5.run
+%%PORTDOCS%%share/tinker/bench/bench5.xyz
 %%PORTDOCS%%share/tinker/bench/results-2.3
 %%PORTDOCS%%share/tinker/bench/results-2.4
 %%PORTDOCS%%share/tinker/bench/results-2.9
@@ -134,11 +142,11 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/bench/results-3.5
 %%PORTDOCS%%share/tinker/bench/results-3.7
 %%PORTDOCS%%share/tinker/bench/results-3.8
+%%PORTDOCS%%share/tinker/bench/results-3.9
 %%PORTDOCS%%share/tinker/params/README
 %%PORTDOCS%%share/tinker/params/amber.prm
-%%PORTDOCS%%share/tinker/params/amberN.prm
 %%PORTDOCS%%share/tinker/params/charmm.prm
-%%PORTDOCS%%share/tinker/params/emr.prm
+%%PORTDOCS%%share/tinker/params/dudek.prm
 %%PORTDOCS%%share/tinker/params/hoch.prm
 %%PORTDOCS%%share/tinker/params/mm2.prm
 %%PORTDOCS%%share/tinker/params/mm3.prm
@@ -147,7 +155,6 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/params/oplsaa.prm
 %%PORTDOCS%%share/tinker/params/smooth.prm
 %%PORTDOCS%%share/tinker/params/smoothaa.prm
-%%PORTDOCS%%share/tinker/params/tinker.prm
 %%PORTDOCS%%share/tinker/params/water.prm
 %%PORTDOCS%%share/tinker/rasmol/rasmol.hlp
 %%PORTDOCS%%share/tinker/test/README
@@ -167,10 +174,8 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/bdna.seq
 %%PORTDOCS%%share/tinker/test/bdna.xyz
 %%PORTDOCS%%share/tinker/test/bearing.key
-%%PORTDOCS%%share/tinker/test/bearing.pdb
 %%PORTDOCS%%share/tinker/test/bearing.xyz
 %%PORTDOCS%%share/tinker/test/bearing2.key
-%%PORTDOCS%%share/tinker/test/bearing2.pdb
 %%PORTDOCS%%share/tinker/test/bearing2.xyz
 %%PORTDOCS%%share/tinker/test/benzene.int
 %%PORTDOCS%%share/tinker/test/benzene.key
@@ -212,10 +217,11 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/calmodulin.pdb
 %%PORTDOCS%%share/tinker/test/calmodulin.seq
 %%PORTDOCS%%share/tinker/test/calmodulin.xyz
+%%PORTDOCS%%share/tinker/test/copper.key
+%%PORTDOCS%%share/tinker/test/copper.xyz
 %%PORTDOCS%%share/tinker/test/cpentene.key
 %%PORTDOCS%%share/tinker/test/cpentene.xyz
 %%PORTDOCS%%share/tinker/test/crambin.key
-%%PORTDOCS%%share/tinker/test/crambin.min
 %%PORTDOCS%%share/tinker/test/crambin.pdb
 %%PORTDOCS%%share/tinker/test/crambin.seq
 %%PORTDOCS%%share/tinker/test/crambin.super
@@ -235,15 +241,15 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/cyclo2.int
 %%PORTDOCS%%share/tinker/test/cyclo2.key
 %%PORTDOCS%%share/tinker/test/cyclo2.xyz
+%%PORTDOCS%%share/tinker/test/dang.key
+%%PORTDOCS%%share/tinker/test/dang.xyz
+%%PORTDOCS%%share/tinker/test/diamond.key
+%%PORTDOCS%%share/tinker/test/diamond.xyz
 %%PORTDOCS%%share/tinker/test/diene.int
 %%PORTDOCS%%share/tinker/test/diene.key
 %%PORTDOCS%%share/tinker/test/diene.xyz
 %%PORTDOCS%%share/tinker/test/dimethane.key
 %%PORTDOCS%%share/tinker/test/dimethane.xyz
-%%PORTDOCS%%share/tinker/test/diwater.key
-%%PORTDOCS%%share/tinker/test/diwater.lin
-%%PORTDOCS%%share/tinker/test/diwater.min
-%%PORTDOCS%%share/tinker/test/diwater.xyz
 %%PORTDOCS%%share/tinker/test/enkephalin.int
 %%PORTDOCS%%share/tinker/test/enkephalin.key
 %%PORTDOCS%%share/tinker/test/enkephalin.make
@@ -277,8 +283,13 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/furan.xyz
 %%PORTDOCS%%share/tinker/test/glucose.key
 %%PORTDOCS%%share/tinker/test/glucose.xyz
+%%PORTDOCS%%share/tinker/test/graphite.key
+%%PORTDOCS%%share/tinker/test/graphite.xyz
+%%PORTDOCS%%share/tinker/test/helix.dyn
 %%PORTDOCS%%share/tinker/test/helix.key
 %%PORTDOCS%%share/tinker/test/helix.xyz
+%%PORTDOCS%%share/tinker/test/heme.key
+%%PORTDOCS%%share/tinker/test/heme.xyz
 %%PORTDOCS%%share/tinker/test/hexane.int
 %%PORTDOCS%%share/tinker/test/hexane.key
 %%PORTDOCS%%share/tinker/test/hexane.xyz
@@ -305,6 +316,7 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/methanol.xyz
 %%PORTDOCS%%share/tinker/test/nacl.key
 %%PORTDOCS%%share/tinker/test/nacl.xyz
+%%PORTDOCS%%share/tinker/test/naphthalene.int
 %%PORTDOCS%%share/tinker/test/naphthalene.key
 %%PORTDOCS%%share/tinker/test/naphthalene.xyz
 %%PORTDOCS%%share/tinker/test/nma.int
@@ -324,21 +336,17 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/octane2.xyz
 %%PORTDOCS%%share/tinker/test/octene.key
 %%PORTDOCS%%share/tinker/test/octene.xyz
+%%PORTDOCS%%share/tinker/test/palmitate.int
 %%PORTDOCS%%share/tinker/test/palmitate.key
 %%PORTDOCS%%share/tinker/test/palmitate.xyz
 %%PORTDOCS%%share/tinker/test/peptide.int
 %%PORTDOCS%%share/tinker/test/peptide.key
 %%PORTDOCS%%share/tinker/test/peptide.make
-%%PORTDOCS%%share/tinker/test/peptide.min
 %%PORTDOCS%%share/tinker/test/peptide.pdb
 %%PORTDOCS%%share/tinker/test/peptide.seq
 %%PORTDOCS%%share/tinker/test/peptide.xyz
 %%PORTDOCS%%share/tinker/test/phenanth.key
 %%PORTDOCS%%share/tinker/test/phenanth.xyz
-%%PORTDOCS%%share/tinker/test/photo.key
-%%PORTDOCS%%share/tinker/test/photo.pdb
-%%PORTDOCS%%share/tinker/test/photo.seq
-%%PORTDOCS%%share/tinker/test/photo.xyz
 %%PORTDOCS%%share/tinker/test/propane.key
 %%PORTDOCS%%share/tinker/test/propane.ray
 %%PORTDOCS%%share/tinker/test/propane.xyz
@@ -369,6 +377,10 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/thr.int
 %%PORTDOCS%%share/tinker/test/thr.key
 %%PORTDOCS%%share/tinker/test/thr.xyz
+%%PORTDOCS%%share/tinker/test/tip3p.key
+%%PORTDOCS%%share/tinker/test/tip3p.xyz
+%%PORTDOCS%%share/tinker/test/tip4p.key
+%%PORTDOCS%%share/tinker/test/tip4p.xyz
 %%PORTDOCS%%share/tinker/test/tip5p.key
 %%PORTDOCS%%share/tinker/test/tip5p.xyz
 %%PORTDOCS%%share/tinker/test/water.int