refine with ssbond

[django_unres.git] / files / refine.sh

diff --git a/files/refine.sh b/files/refine.sh
index e7e3b4a..c039354 100755 (executable)
--- a/files/refine.sh
+++ b/files/refine.sh
@@ -4,9 +4,34 @@
 export AMBERHOME=/users2/local/amber/amber14
 export LD_LIBRARY_PATH=/users2/local/lib/intel/composer_xe_2015/intel64:${LD_LIBRARY_PATH}
 
-rm -f tmp1.pdb
+rm -f tmp1.pdb tmp1
 ln -s $1 tmp1.pdb
-$AMBERHOME/bin/tleap -f /users2/CASP12/EXAMPLES/all-atom/amber_files/leap.bat
+
+cat << EOF >leap.bat
+source leaprc.ff14SB
+xx3 = loadpdb tmp1.pdb
+EOF
+
+pdb=$1 
+shift  
+while true; do
+       if [ $1 ]; then
+                echo bond xx3.$1.SG xx3.$2.SG >> leap.bat
+                awk -v ires=$1 -f ../files/cyx.awk $pdb > tmp1
+                awk -v ires=$2 -f ../files/cyx.awk tmp1 > $pdb
+                shift
+                shift
+       else
+               break 
+       fi
+done
+cat << EOF >> leap.bat
+saveamberparm xx3 t.top t.crd
+savepdb xx3 z_tleap.pdb
+quit
+EOF
+
+$AMBERHOME/bin/tleap -f leap.bat
 
 /users2/local/mmtsb/perl/convpdb.pl -out generic_noh z_tleap.pdb > noh.pdb
 /users2/local/pymol_1.6/pymol -cq /users2/CASP12/EXAMPLES/all-atom/amber_refine/dss.py | awk \
@@ -19,12 +44,12 @@ $AMBERHOME/bin/tleap -f /users2/CASP12/EXAMPLES/all-atom/amber_files/leap.bat
 /users/software/openmpi-1.8.4/bin/mpirun \
 -machinefile $PBS_NODEFILE -np 4 \
 $AMBERHOME/bin/sander.MPI \
--O -i /users2/CASP12/EXAMPLES/all-atom/amber_files/min1.in -p t.top -o amber_min_$1.out \
+-O -i /users2/CASP12/EXAMPLES/all-atom/amber_files/min1.in -p t.top -o amber_min_$pdb.out \
 -c t.crd -ref t.crd
 
 $AMBERHOME/bin/ambpdb -p t.top <restrt> stop.pdb
 
-rm $1
-/users2/local/mmtsb/perl/convpdb.pl -amber -out generic_noh stop.pdb > $1
+rm $pdb
+/users2/local/mmtsb/perl/convpdb.pl -amber -out generic_noh stop.pdb > $pdb
 rm tmp1.pdb z_tleap.pdb t.top t.crd leap.log noh.pdb zakresy.csv RST.dat restrt mdinfo stop.pdb