Maintainer update of biology/tinker port to version 4.0.

PR:		52498
Submitted by:	Glenn Johnson <gjohnson@srrc.ars.usda.gov>

5 files changed, 42 insertions, 20 deletions

diff --git a/biology/tinker/Makefile b/biology/tinker/Makefile
index fe25635b5bca..1ff1a6f3b76d 100644
--- a/biology/tinker/Makefile
+++ b/biology/tinker/Makefile
@@ -6,8 +6,7 @@
 #
 
 PORTNAME=	tinker
-PORTVERSION=	3.9
-PORTREVISION=	1
+PORTVERSION=	4.0
 CATEGORIES=	biology
 MASTER_SITES=	ftp://dasher.wustl.edu/pub/
 DISTNAME=	${PORTNAME}
@@ -25,11 +24,6 @@ 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} ""
-
 .include <bsd.port.pre.mk>
 
 .if defined(WITH_VIEWER)
diff --git a/biology/tinker/files/patch-aa b/biology/tinker/files/patch-aa
index 0fc53910ba6b..6f83ecacd6dd 100644
--- a/biology/tinker/files/patch-aa
+++ b/biology/tinker/files/patch-aa
@@ -1,5 +1,5 @@
---- ../make/Makefile.orig	Tue Nov 13 10:16:27 2001
-+++ ../make/Makefile	Mon Dec 31 15:33:40 2001
+--- ../make/Makefile.orig	Wed Nov 14 01:16:27 2001
++++ ../make/Makefile	Sat Jul 19 12:22:51 2003
 @@ -9,8 +9,8 @@
  ##
  ##   1. make all              Build all the TINKER executables
diff --git a/biology/tinker/files/patch-openend.f b/biology/tinker/files/patch-openend.f
new file mode 100644
index 000000000000..a34260872792
--- /dev/null
+++ b/biology/tinker/files/patch-openend.f
@@ -0,0 +1,11 @@
+--- openend.f.orig	Tue Dec 18 12:28:54 2001
++++ openend.f	Sat Jul 19 12:30:57 2003
+@@ -33,7 +33,7 @@
+ c
+ c     common extension supported by many Fortran 77 compilers
+ c
+-c     open (unit=iunit,file=name,status='old',access='append')
++      open (unit=iunit,file=name,status='old',access='append')
+ c
+ c     some Fortran 77 compilers open files for append by default
+ c
diff --git a/biology/tinker/pkg-plist b/biology/tinker/pkg-plist
index d84db098a538..ed19ce608489 100644
--- a/biology/tinker/pkg-plist
+++ b/biology/tinker/pkg-plist
@@ -13,8 +13,6 @@ bin/intedit
 bin/intxyz
 bin/minimize
 bin/minirot
-bin/minrigid
-bin/monte
 bin/newton
 bin/newtrot
 bin/nucleic
@@ -45,6 +43,8 @@ bin/timerot
 bin/vibrate
 bin/vibrot
 bin/xtalfit
+bin/vibrot
+bin/xtalfit
 bin/xtalmin
 bin/xyzedit
 bin/xyzint
diff --git a/biology/tinker/pkg-plist.viewer b/biology/tinker/pkg-plist.viewer
index 98ee34b042da..f21859c26219 100644
--- a/biology/tinker/pkg-plist.viewer
+++ b/biology/tinker/pkg-plist.viewer
@@ -61,6 +61,8 @@ bin/xyzsybyl
 %%PORTDOCS%%share/doc/tinker/license.pdf
 %%PORTDOCS%%share/doc/tinker/license.ps
 %%PORTDOCS%%share/doc/tinker/license.txt
+%%PORTDOCS%%share/doc/tinker/logo-bind.pdf
+%%PORTDOCS%%share/doc/tinker/logo-bind.ps.gz
 %%PORTDOCS%%share/doc/tinker/logo.pdf
 %%PORTDOCS%%share/doc/tinker/logo.ps.gz
 %%PORTDOCS%%share/doc/tinker/release-3.2
@@ -68,6 +70,7 @@ bin/xyzsybyl
 %%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/release-4.0
 %%PORTDOCS%%share/doc/tinker/summary.pdf
 %%PORTDOCS%%share/doc/tinker/summary.ps
 %%PORTDOCS%%share/doc/tinker/summary.txt
@@ -144,15 +147,21 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/bench/results-3.7
 %%PORTDOCS%%share/tinker/bench/results-3.8
 %%PORTDOCS%%share/tinker/bench/results-3.9
+%%PORTDOCS%%share/tinker/bench/results-4.0
 share/tinker/params/README
-share/tinker/params/amber.prm
-share/tinker/params/charmm.prm
+share/tinker/params/amber94.prm
+share/tinker/params/amber96.prm
+share/tinker/params/amber98.prm
+share/tinker/params/amoeba.prm
+share/tinker/params/charmm19.prm
+share/tinker/params/charmm27.prm
+share/tinker/params/dudek.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/oplsua.prm
 share/tinker/params/smooth.prm
 share/tinker/params/smoothaa.prm
 share/tinker/params/water.prm
@@ -162,6 +171,8 @@ share/tinker/rasmol/rasmol.hlp
 %%PORTDOCS%%share/tinker/test/ala20.xyz
 %%PORTDOCS%%share/tinker/test/alkane.key
 %%PORTDOCS%%share/tinker/test/alkane.xyz
+%%PORTDOCS%%share/tinker/test/amoeba.key
+%%PORTDOCS%%share/tinker/test/amoeba.xyz
 %%PORTDOCS%%share/tinker/test/arach.int
 %%PORTDOCS%%share/tinker/test/arach.key
 %%PORTDOCS%%share/tinker/test/arach.xyz
@@ -227,7 +238,6 @@ share/tinker/rasmol/rasmol.hlp
 %%PORTDOCS%%share/tinker/test/crambin.key
 %%PORTDOCS%%share/tinker/test/crambin.pdb
 %%PORTDOCS%%share/tinker/test/crambin.seq
-%%PORTDOCS%%share/tinker/test/crambin.super
 %%PORTDOCS%%share/tinker/test/crambin.xyz
 %%PORTDOCS%%share/tinker/test/crambinx.key
 %%PORTDOCS%%share/tinker/test/crambinx.ray
@@ -253,9 +263,6 @@ share/tinker/rasmol/rasmol.hlp
 %%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.xyz
 %%PORTDOCS%%share/tinker/test/enkephalin.int
 %%PORTDOCS%%share/tinker/test/enkephalin.key
 %%PORTDOCS%%share/tinker/test/enkephalin.make
@@ -290,6 +297,9 @@ share/tinker/rasmol/rasmol.hlp
 %%PORTDOCS%%share/tinker/test/furan.xyz
 %%PORTDOCS%%share/tinker/test/glucose.key
 %%PORTDOCS%%share/tinker/test/glucose.xyz
+%%PORTDOCS%%share/tinker/test/glycerol.dyn
+%%PORTDOCS%%share/tinker/test/glycerol.key
+%%PORTDOCS%%share/tinker/test/glycerol.xyz
 %%PORTDOCS%%share/tinker/test/graphite.key
 %%PORTDOCS%%share/tinker/test/graphite.xyz
 %%PORTDOCS%%share/tinker/test/helix.dyn
@@ -304,7 +314,6 @@ share/tinker/rasmol/rasmol.hlp
 %%PORTDOCS%%share/tinker/test/hexanes.key
 %%PORTDOCS%%share/tinker/test/hexanes.run
 %%PORTDOCS%%share/tinker/test/hexanes.xyz
-%%PORTDOCS%%share/tinker/test/hexanex.xyz
 %%PORTDOCS%%share/tinker/test/imidazole.int
 %%PORTDOCS%%share/tinker/test/imidazole.key
 %%PORTDOCS%%share/tinker/test/imidazole.xyz
@@ -362,6 +371,10 @@ share/tinker/rasmol/rasmol.hlp
 %%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/pol3.key
 %%PORTDOCS%%share/tinker/test/pol3.xyz
 %%PORTDOCS%%share/tinker/test/propane.key
@@ -402,6 +415,10 @@ share/tinker/rasmol/rasmol.hlp
 %%PORTDOCS%%share/tinker/test/tip4p.xyz
 %%PORTDOCS%%share/tinker/test/tip5p.key
 %%PORTDOCS%%share/tinker/test/tip5p.xyz
+%%PORTDOCS%%share/tinker/test/trpcage.key
+%%PORTDOCS%%share/tinker/test/trpcage.pdb
+%%PORTDOCS%%share/tinker/test/trpcage.seq
+%%PORTDOCS%%share/tinker/test/trpcage.xyz
 %%PORTDOCS%%share/tinker/test/water.int
 %%PORTDOCS%%share/tinker/test/water.key
 %%PORTDOCS%%share/tinker/test/water.xyz
@@ -428,7 +445,7 @@ share/tinker/tinker.txt
 %%PORTDOCS%%@dirrm share/doc/tinker
 %%PORTDOCS%%@dirrm share/examples/tinker
 %%PORTDOCS%%@dirrm share/tinker/bench
-@dirrm share/tinker/params
 @dirrm share/tinker/rasmol
+@dirrm share/tinker/params
 %%PORTDOCS%%@dirrm share/tinker/test
 @dirrm share/tinker