X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=files%2Fpbs8.csh;h=0e3867dba89f1824165dfccbbce729ae33d5fd0a;hb=e965db4a237f05d8ef5d1aa56b2494d1c54c067b;hp=d7ec50715cd71b00ccf3415119684f25b794215a;hpb=0af8cfed9da05d1e01aa7d2f6d702c3a8613c177;p=django_unres.git

diff --git a/files/pbs8.csh b/files/pbs8.csh
index d7ec507..0e3867d 100755
--- a/files/pbs8.csh
+++ b/files/pbs8.csh
@@ -70,13 +70,24 @@ $MPIRUN -machinefile $PBS_NODEFILE -np 2 $CLUSTER_WHAM_BIN
 ln -s file_wham_T*K_ave.pdb ave
 ../files/cluster2allatom.sh ave
 rm ave
+
+#amber min refinement
+foreach i (`seq 1 5`)
+../files/refine.sh MODEL$i.pdb $ssbond
+end
+
 /users2/local/pymol_1.6/pymol -c ../files/model.pml
 
-/users2/local/bin/tmscore MODEL1.pdb plik.pdb > tmscore1.out
-/users2/local/bin/tmscore MODEL2.pdb plik.pdb > tmscore2.out
-/users2/local/bin/tmscore MODEL3.pdb plik.pdb > tmscore3.out
-/users2/local/bin/tmscore MODEL4.pdb plik.pdb > tmscore4.out
-/users2/local/bin/tmscore MODEL5.pdb plik.pdb > tmscore5.out
+awk '{printf "%s%s%s\n",substr($0,0,21)," ",substr($0,23)}' plik.pdb > tmp.pdb
+/users2/local/mmtsb/perl/convpdb.pl -renumber 1 -out generic tmp.pdb > plik1.pdb
+rm tmp.pdb
+
+/users2/local/bin/tmscore MODEL1.pdb plik1.pdb > tmscore1.out
+/users2/local/bin/tmscore MODEL2.pdb plik1.pdb > tmscore2.out
+/users2/local/bin/tmscore MODEL3.pdb plik1.pdb > tmscore3.out
+/users2/local/bin/tmscore MODEL4.pdb plik1.pdb > tmscore4.out
+/users2/local/bin/tmscore MODEL5.pdb plik1.pdb > tmscore5.out
+rm plik1.pdb
 
 #END
 touch finished