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))
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)))
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: