control_line = 'SEED='+str(instance.md_seed)+' ' \
+ instance.min_choice \
- + ' pdbstart pdbref BOXX=1000. BOXY=1000. BOXZ=1000. '
+ + ' pdbstart pdbref ' \
+ + ' BOXX='+str(instance.boxx) \
+ + ' BOXY='+str(instance.boxy) \
+ + ' BOXZ='+str(instance.boxz) +' '
if not instance.min_overlap:
control_line = control_line+'overlap '
if not instance.min_searchsc:
if instance.type == 'md' :
control_line = 'SEED='+str(instance.md_seed)+' '\
- +instance.md_start +' md one_letter BOXX=1000. BOXY=1000. BOXZ=1000. '
+ +instance.md_start +' md one_letter'\
+ + ' BOXX='+str(instance.boxx) \
+ + ' BOXY='+str(instance.boxy) \
+ + ' BOXZ='+str(instance.boxz) +' '
+
if instance.md_pdbref:
control_line = control_line+'pdbref '
if instance.type == 'remd' :
control_line = 'SEED='+str(instance.md_seed)+' '\
- +instance.md_start +' re one_letter BOXX=1000. BOXY=1000. BOXZ=1000. '
+ +instance.md_start +' re one_letter'\
+ + ' BOXX='+str(instance.boxx) \
+ + ' BOXY='+str(instance.boxy) \
+ + ' BOXZ='+str(instance.boxz) +' '
+
if instance.md_pdbref:
control_line = control_line+'pdbref '
f1 = open('../files/pbs_md_new.csh', 'r')
f2 = open('pbs.csh', 'w')
for line in f1:
- f2.write(line.replace('$dimen3',str(dimen3) ))
+ f2.write(line.replace('$dimen3',str(dimen3)+' '+str(instance.md_temp) ))
f1.close()
f2.close()
pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta)
tmp_ss=''
- ix=0
- if seq[0]=='X':
- ix=1
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)
- l.append(e[1]-ix)
+ l.append(e[0]-ix[e[0]])
+ l.append(e[1]-ix[e[1]])
tmp_ss=' '.join(map(str,l))
os.chdir(instance.jobdirname)
isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000)
if instance.md_pdbref:
- f.write('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
- ' einicheck=1 rescale=2 delta=0.02 cxfile classify\n')
+ f.write('{:79}'.format('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
+ ' einicheck=1 rescale=2 delta=0.02 cxfile classify')+'&\n')
+ f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
+ ' BOXZ='+str(instance.boxz) +'\n')
else:
- f.write('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
- ' einicheck=1 rescale=2 delta=0.02 cxfile\n')
+ f.write('{:79}'.format('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
+ ' einicheck=1 rescale=2 delta=0.02 cxfile')+'&\n')
+ f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
+ ' BOXZ='+str(instance.boxz) +'\n')
f.write('nres='+str(len(seq))+' one_letter\n')
for i in range(0,len(seq),80):
f.write(seq[i:i+80]+'\n')
with open(instance.jobdirname+'/file_cluster.inp','w') as f:
f.write(instance.name + ' UNRES server job'+ '\n')
- f.write('nres='+str(len(seq))
+ f.write('{:79}'.format('nres='+str(len(seq))
+' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1'
- +' temper='+str(instance.remd_cluter_temp)+'\n')
+ +' temper='+str(instance.remd_cluter_temp))+'&\n')
+ f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
+ ' BOXZ='+str(instance.boxz) +'\n')
f.write(w)
for i in range(0,len(seq),80):
f.write(seq[i:i+80]+'\n')