remd - amber all atom min refinement

[django_unres.git] / files / refine.sh

diff --git a/files/refine.sh b/files/refine.sh
new file mode 100755 (executable)
index 0000000..23a022e
--- /dev/null
+++ b/files/refine.sh
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+#!/bin/sh
+# refine.sh plik.pdb
+
+export AMBERHOME=/opt/amber12
+export LD_LIBRARY_PATH=/opt/lib/intel/11.1:/big/appl/lib/
+
+rm -f tmp1.pdb
+ln -s $1 tmp1.pdb
+$AMBERHOME/bin/tleap -f /big/appl/amber_refine/leap.bat
+
+/big/appl/mmtsb/perl/convpdb.pl -out generic_noh z_tleap.pdb > noh.pdb
+/opt/pymol-svn/pymol -cq /big/appl/amber_refine/dss.py | awk \
+'{ires[NR]=$2;ss[NR]=$3}END{for (i=2;i<=NR;i++) {if (ss[i-1]!=ss[i]&&ss[i-1]=="L") printf "%s;",ires[i];if (ss[i-1]!=ss[i]&&ss[i]=="L") printf "%s;%s\n",ires[i-1],ss[i-1]}}' \
+> zakresy.csv
+
+
+/big/appl/amber_refine/narzuc_RST.pl z_tleap.pdb
+
+/opt/mpich2-1.4.1p1_intel/bin/mpirun \
+-machinefile $PBS_NODEFILE -np 4 \
+$AMBERHOME/bin/sander.MPI \
+-O -i /big/appl/amber_refine/min1.in -p t.top -o amber_min_$1.out \
+-c t.crd -ref t.crd
+
+$AMBERHOME/bin/ambpdb -p t.top <restrt> stop.pdb
+
+rm $1
+/big/appl/mmtsb/perl/convpdb.pl -amber -out generic_noh stop.pdb > $1
+rm tmp1.pdb z_tleap.pdb t.top t.crd leap.log noh.pdb zakresy.csv RST.dat restrt mdinfo stop.pdb
+