+ ' BOXZ='+str(instance.boxz) +' '
if instance.type == 'dock':
- control_line = control_line+'CONSTR_HOMOL=20 '
+ control_line = control_line+'CONSTR_HOMOL=24 '
if instance.md_pdbref:
control_line = control_line+'pdbref '
f.write('READ2SIGMA START_FROM_MODELS\n')
for i in range(1,10):
f.write('model0'+str(i)+'.pdb\n')
- for i in range(10,21):
+ for i in range(10,25):
f.write('model'+str(i)+'.pdb\n')
if instance.type == 'md' and instance.md_start != 'pdbstart':
elif 'cd $PBS_O_WORKDIR' in line and instance.type == 'dock':
f2.write(line)
if instance.dock_peptide:
- f2.write('../files/generator_v12a plik.pdb plik2.pdb 1 \n')
+ f2.write('../files/generator_v13 plik.pdb plik2.pdb 1 \n')
else:
- f2.write('../files/generator_v12a plik.pdb plik2.pdb 0 \n')
+ f2.write('../files/generator_v13 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")
if instance.md_2d != '':
f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
if instance.type == 'dock':
- f.write('{:79}'.format(' n_ene=19 CONSTR_HOMOL=20')+'&\n')
+ f.write('{:79}'.format(' n_ene=19 CONSTR_HOMOL=24')+'&\n')
if instance.unres_ff =='NEWCT-9P':
f.write('{:79}'.format('tormode=2 ')+'&\n')
f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
f.write('READ2SIGMA \n')
for i in range(1,10):
f.write('model0'+str(i)+'.pdb\n')
- for i in range(10,21):
+ for i in range(10,25):
f.write('model'+str(i)+'.pdb\n')
if instance.md_2d != '':
if instance.md_2d != '':
f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
if instance.type == 'dock':
- f.write('{:79}'.format(' CONSTR_HOMOL=20')+'&\n')
+ f.write('{:79}'.format(' CONSTR_HOMOL=24')+'&\n')
if instance.unres_ff =='NEWCT-9P':
f.write('{:79}'.format('tormode=2 ')+'&\n')
f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
f.write('READ2SIGMA \n')
for i in range(1,10):
f.write('model0'+str(i)+'.pdb\n')
- for i in range(10,21):
+ for i in range(10,25):
f.write('model'+str(i)+'.pdb\n')
if instance.md_2d != '':
f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))