update from 3.7 to 3.8

PR:		24371
Submitted by:	MAINTAINER

1 files changed, 106 insertions, 57 deletions

diff --git a/biology/tinker/pkg-plist b/biology/tinker/pkg-plist
index 012299f88e88..880a1d1110ce 100644
--- a/biology/tinker/pkg-plist
+++ b/biology/tinker/pkg-plist
@@ -4,6 +4,7 @@ bin/anneal
 bin/archive
 bin/correlate
 bin/crystal
+bin/diffuse
 bin/distgeom
 bin/document
 bin/dynamic
@@ -12,8 +13,10 @@ bin/intedit
 bin/intxyz
 bin/minimize
 bin/minirot
+bin/minrigid
 bin/newton
 bin/newtrot
+bin/nucleic
 bin/optimize
 bin/optirot
 bin/optrigid
@@ -23,10 +26,12 @@ bin/protein
 bin/pss
 bin/pssrigid
 bin/pssrot
+bin/radial
 bin/saddle
 bin/scan
 bin/sniffer
 bin/spacefill
+bin/spectrum
 bin/superpose
 bin/sybylxyz
 bin/testgrad
@@ -43,95 +48,92 @@ bin/xyzedit
 bin/xyzint
 bin/xyzpdb
 bin/xyzsybyl
-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/doc/tinker/README
+share/doc/tinker/announce.txt
 share/doc/tinker/guide.pdf
-share/doc/tinker/guide.ps.Z
+share/doc/tinker/guide.ps.gz
 share/doc/tinker/guide.txt
 share/doc/tinker/license.pdf
-share/doc/tinker/license.ps.Z
+share/doc/tinker/license.ps
 share/doc/tinker/license.txt
-share/doc/tinker/logo.ps.Z
-share/doc/tinker/spine.ps
+share/doc/tinker/logo.pdf
+share/doc/tinker/logo.ps.gz
 share/doc/tinker/summary.pdf
 share/doc/tinker/summary.ps
 share/doc/tinker/summary.txt
 share/examples/tinker/README
+share/examples/tinker/anion.dat
 share/examples/tinker/anion.dyn0
-share/examples/tinker/anion.in1
-share/examples/tinker/anion.in2
 share/examples/tinker/anion.key
 share/examples/tinker/anion.log
 share/examples/tinker/anion.run
 share/examples/tinker/anion.xyz
 share/examples/tinker/argon.1st
-share/examples/tinker/argon.in1
-share/examples/tinker/argon.in2
 share/examples/tinker/argon.key
 share/examples/tinker/argon.log
 share/examples/tinker/argon.run
 share/examples/tinker/clean.make
-share/examples/tinker/cluster.in1
+share/examples/tinker/cluster.dat
 share/examples/tinker/cluster.key
 share/examples/tinker/cluster.log
 share/examples/tinker/cluster.run
 share/examples/tinker/cluster.xyz
-share/examples/tinker/crambin.in1
-share/examples/tinker/crambin.in2
-share/examples/tinker/crambin.in3
 share/examples/tinker/crambin.key
 share/examples/tinker/crambin.log
 share/examples/tinker/crambin.pdb
 share/examples/tinker/crambin.run
 share/examples/tinker/cyclohex.boat
 share/examples/tinker/cyclohex.chair
-share/examples/tinker/cyclohex.in1
-share/examples/tinker/cyclohex.in2
-share/examples/tinker/cyclohex.in3
 share/examples/tinker/cyclohex.key
 share/examples/tinker/cyclohex.log
 share/examples/tinker/cyclohex.run
-share/examples/tinker/enkephalin.in1
-share/examples/tinker/enkephalin.in2
-share/examples/tinker/enkephalin.in3
+share/examples/tinker/enkephalin.dat
 share/examples/tinker/enkephalin.key
 share/examples/tinker/enkephalin.log
 share/examples/tinker/enkephalin.run
 share/examples/tinker/formamide.cell
-share/examples/tinker/formamide.in1
-share/examples/tinker/formamide.in2
-share/examples/tinker/formamide.in3
-share/examples/tinker/formamide.in4
+share/examples/tinker/formamide.dat
 share/examples/tinker/formamide.key
 share/examples/tinker/formamide.log
 share/examples/tinker/formamide.run
-share/examples/tinker/helix.in1
+share/examples/tinker/helix.1st
 share/examples/tinker/helix.key
 share/examples/tinker/helix.log
 share/examples/tinker/helix.run
-share/examples/tinker/helix.xyz
+share/examples/tinker/salt.cell
+share/examples/tinker/salt.key
+share/examples/tinker/salt.log
+share/examples/tinker/salt.run
+share/tinker/bench/bench-1.key
+share/tinker/bench/bench-1.run
+share/tinker/bench/bench-1.xyz
+share/tinker/bench/bench-2.key
+share/tinker/bench/bench-2.run
+share/tinker/bench/bench-2.xyz
+share/tinker/bench/bench-3.key
+share/tinker/bench/bench-3.run
+share/tinker/bench/bench-3.xyz
+share/tinker/bench/bench-4.dyn0
+share/tinker/bench/bench-4.key
+share/tinker/bench/bench-4.log
+share/tinker/bench/bench-4.run
+share/tinker/bench/bench-4.xyz
+share/tinker/bench/bench-5.dyn0
+share/tinker/bench/bench-5.key
+share/tinker/bench/bench-5.run
+share/tinker/bench/bench-5.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/results-3.8
 share/tinker/params/README
 share/tinker/params/amber.prm
+share/tinker/params/amberN.prm
 share/tinker/params/charmm.prm
 share/tinker/params/emr.prm
 share/tinker/params/hoch.prm
@@ -147,19 +149,18 @@ share/tinker/params/water.prm
 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/alkane.key
+share/tinker/test/alkane.xyz
 share/tinker/test/arach.int
 share/tinker/test/arach.key
 share/tinker/test/arach.xyz
 share/tinker/test/azulene.int
 share/tinker/test/azulene.key
 share/tinker/test/azulene.xyz
+share/tinker/test/bdna.int
+share/tinker/test/bdna.key
+share/tinker/test/bdna.seq
+share/tinker/test/bdna.xyz
 share/tinker/test/bearing.key
 share/tinker/test/bearing.pdb
 share/tinker/test/bearing.xyz
@@ -169,6 +170,13 @@ share/tinker/test/bearing2.xyz
 share/tinker/test/benzene.int
 share/tinker/test/benzene.key
 share/tinker/test/benzene.xyz
+share/tinker/test/bowl.int
+share/tinker/test/bowl.key
+share/tinker/test/bowl.xyz
+share/tinker/test/bowl2.key
+share/tinker/test/bowl2.xyz
+share/tinker/test/bowl3.key
+share/tinker/test/bowl3.xyz
 share/tinker/test/butane.int
 share/tinker/test/butane.key
 share/tinker/test/butane.xyz
@@ -195,13 +203,20 @@ share/tinker/test/c7ax.xyz
 share/tinker/test/c7eq.key
 share/tinker/test/c7eq.seq
 share/tinker/test/c7eq.xyz
+share/tinker/test/calmodulin.key
+share/tinker/test/calmodulin.pdb
+share/tinker/test/calmodulin.seq
+share/tinker/test/calmodulin.xyz
 share/tinker/test/cpentene.key
 share/tinker/test/cpentene.xyz
 share/tinker/test/crambin.key
+share/tinker/test/crambin.min
 share/tinker/test/crambin.pdb
 share/tinker/test/crambin.seq
+share/tinker/test/crambin.super
 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
@@ -221,12 +236,12 @@ 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
@@ -237,14 +252,21 @@ share/tinker/test/ester.xyz
 share/tinker/test/ethane.int
 share/tinker/test/ethane.key
 share/tinker/test/ethane.xyz
+share/tinker/test/ethanol.int
+share/tinker/test/ethanol.key
+share/tinker/test/ethanol.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/formamide.key
-share/tinker/test/formamide.xyz
+share/tinker/test/form.key
+share/tinker/test/form.xyz
+share/tinker/test/formbig.key
+share/tinker/test/formbig.xyz
+share/tinker/test/formbox.key
+share/tinker/test/formbox.xyz
 share/tinker/test/furan.int
 share/tinker/test/furan.key
 share/tinker/test/furan.xyz
@@ -252,6 +274,13 @@ share/tinker/test/glucose.key
 share/tinker/test/glucose.xyz
 share/tinker/test/helix.key
 share/tinker/test/helix.xyz
+share/tinker/test/hexane.int
+share/tinker/test/hexane.key
+share/tinker/test/hexane.xyz
+share/tinker/test/hexanes.dyn
+share/tinker/test/hexanes.key
+share/tinker/test/hexanes.run
+share/tinker/test/hexanes.xyz
 share/tinker/test/imidazole.int
 share/tinker/test/imidazole.key
 share/tinker/test/imidazole.xyz
@@ -260,11 +289,19 @@ share/tinker/test/imine.key
 share/tinker/test/imine.xyz
 share/tinker/test/lactam.key
 share/tinker/test/lactam.xyz
+share/tinker/test/melittin.key
+share/tinker/test/melittin.pdb
+share/tinker/test/melittin.seq
+share/tinker/test/melittin.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/nacl.key
+share/tinker/test/nacl.xyz
+share/tinker/test/naphthalene.key
+share/tinker/test/naphthalene.xyz
 share/tinker/test/nma.int
 share/tinker/test/nma.key
 share/tinker/test/nma.xyz
@@ -287,14 +324,24 @@ share/tinker/test/palmitate.xyz
 share/tinker/test/peptide.int
 share/tinker/test/peptide.key
 share/tinker/test/peptide.make
+share/tinker/test/peptide.min
 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/propane.key
+share/tinker/test/propane.ray
+share/tinker/test/propane.xyz
 share/tinker/test/propellane.int
 share/tinker/test/propellane.key
 share/tinker/test/propellane.xyz
+share/tinker/test/propyne.key
+share/tinker/test/propyne.xyz
 share/tinker/test/pyridine.int
 share/tinker/test/pyridine.key
 share/tinker/test/pyridine.xyz
@@ -317,6 +364,8 @@ share/tinker/test/thiophene.xyz
 share/tinker/test/thr.int
 share/tinker/test/thr.key
 share/tinker/test/thr.xyz
+share/tinker/test/tip5p.key
+share/tinker/test/tip5p.xyz
 share/tinker/test/water.int
 share/tinker/test/water.key
 share/tinker/test/water.xyz
@@ -337,9 +386,9 @@ share/tinker/test/white.int
 share/tinker/test/white.key
 share/tinker/test/white.xyz
 share/tinker/tinker.txt
-@dirrm share/tinker/bench
 @dirrm share/doc/tinker
 @dirrm share/examples/tinker
+@dirrm share/tinker/bench
 @dirrm share/tinker/params
 @dirrm share/tinker/test
 @dirrm share/tinker