X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;ds=sidebyside;f=files%2Fpbs8_new.csh;h=ca528bb128f4198019936ea4702568697aad8997;hb=e965db4a237f05d8ef5d1aa56b2494d1c54c067b;hp=0382652d94a24edb24d09c9b8c08d4304dd23bcb;hpb=533934d3ce690cbee495617d193c7560960e55d5;p=django_unres.git

diff --git a/files/pbs8_new.csh b/files/pbs8_new.csh
index 0382652..ca528bb 100755
--- a/files/pbs8_new.csh
+++ b/files/pbs8_new.csh
@@ -12,7 +12,7 @@ setenv THETPARPDB $DD/thetaml_ext.5parm
 setenv ROTPARPDB $DD/scgauss_ext.parm
 setenv ROTPAR $DD/rotamers_AM1_aura_ext.10022007.parm
 setenv TORPAR $DD/tor_opt_iter1_7p_old-ext.parm
-setenv TORDPAR $DD/pot_tord_G631_DIL_ext.parm
+setenv TORDPAR $DD/torsion_double_631Gdp_old_ext.parm
 setenv ELEPAR $DD/electr_631Gdp_ext.parm
 setenv SIDEPAR $DD/sc_GB_opt_iter1_7p_old-ext_lip.parm
 setenv FOURIER $DD/fourier_opt_iter1_7p_old-ext.parm
@@ -73,16 +73,21 @@ rm ave
 
 #amber min refinement
 foreach i (`seq 1 5`)
-../files/refine.sh MODEL$i.pdb
+../files/refine.sh MODEL$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