+
+ tmp_ss=''
+ if instance.ssbond!='':
+ ix=[]
+ ii=0
+ for i in range(0,len(seq)):
+ if seq[i]=='X':
+ ii=ii+1
+ ix.append(ii)
+ l=[]
+ ss=json.loads(instance.ssbond)
+ for e in ss:
+ l.append(e[0]-ix[e[0]])
+ l.append(e[1]-ix[e[1]])
+ tmp_ss=' '.join(map(str,l))
+
+ os.chdir(instance.jobdirname)
+ if instance.unres_ff =='E0LL2Y':
+ f1 = open('../files/pbs8.csh', 'r')
+ else:
+ f1 = open('../files/pbs8_new.csh', 'r')