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 $DD/fourier_opt_iter1_7p_old-ext.parm
#amber min refinement
foreach i (`seq 1 5`)
-../files/refine.sh MODEL$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