X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=files%2Frefine.sh;h=a997dbc1393db96337d9cbd27e551c765355c933;hb=1c260674ebd5c690868fadea76ecd86e8b7f0b74;hp=c039354adca1509fba448785816fd1f2a43a6136;hpb=ae2ca9f762ec4db6c91066465f347fc3678cddae;p=django_unres.git

diff --git a/files/refine.sh b/files/refine.sh
index c039354..a997dbc 100755
--- a/files/refine.sh
+++ b/files/refine.sh
@@ -34,8 +34,8 @@ 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 \
-'{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]}}' \
+/users2/local/pymol_1.6/pymol -cq /users2/CASP12/EXAMPLES/all-atom/amber_files/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;%s\n",ires[i-1],ss[i-1];if (ss[i-1]!=ss[i]&&ss[i]!="L") printf "%s;",ires[i];}}' \
 > zakresy.csv
 
 
@@ -50,6 +50,7 @@ $AMBERHOME/bin/sander.MPI \
 $AMBERHOME/bin/ambpdb -p t.top <restrt> stop.pdb
 
 rm $pdb
+cp stop.pdb ${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