docking working version

[django_unres.git] / django_simple / todo / jobfiles.py

diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index e38d7ae..9855b31 100644 (file)
--- a/django_simple/todo/jobfiles.py
+++ b/django_simple/todo/jobfiles.py
@@ -272,7 +272,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
 
        if instance.type == 'min' or instance.md_start == 'pdbstart':
           if instance.type == 'dock':
-            f.write('model01.pdb\n')
+            f.write('plik1ter.pdb\n')
           else:  
             f.write('plik.pdb\n')
           f.write(write_ssbond(instance.ssbond))
@@ -408,7 +408,10 @@ CUTOFF=7.00000 WCORR4=0.00000"""
            f2.write(line.replace('$ssbond',tmp_ss))
           elif 'cd $PBS_O_WORKDIR' in line and instance.type == 'dock':
             f2.write(line)
-            f2.write('../files/generator_v7 plik.pdb plik2.pdb\n')
+            f2.write('../files/generator_v12a plik.pdb plik2.pdb 0 \n')
+            f2.write("sed '/END/q' plik.pdb |grep ATOM > plik1ter.pdb \n")
+            f2.write("echo TER >>  plik1ter.pdb \n")
+            f2.write("sed '/END/q' plik2.pdb |grep ATOM >> plik1ter.pdb \n")            
           else:
            tmp1=json.loads(instance.remd_multi_t)
            f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas)))
@@ -497,7 +500,10 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           f.write('file_MD000\n')
           if instance.md_pdbref:
              f.write('pdbref\n')
-             f.write('plik.pdb\n')
+             if instance.type == 'dock':
+              f.write('plik1ter.pdb\n')
+             else:
+              f.write('plik.pdb\n')
 
            
       with open(instance.jobdirname+'/file_cluster.inp','w') as f: