Dear all,
I found the solution to include disulfide bonds, while the later problem is how to combine multiple cpu caculation and including disulfide bridges together? they can be performed indenpendently but not together, could you please give me some suggestion?
model.py
# Example of changing the default optmization schedule
from modeller import *
from modeller.automodel import *
from modeller.parallel import *
j = job(modeller_path="/usr/lib/modeller9v7/bin/modslave.py")
j.append(local_slave()) # 1 Processor
j.append(local_slave()) # 2 Processors
j.append(local_slave()) # 3 Processors
j.append(local_slave()) # 4 Processors
class Mymodel(automodel):
def special_patches(self, aln):
self.patch(residue_type='DISU', residues=(self.residues['151'],self.residues['181']))
self.patch(residue_type='DISU', residues=(self.residues['422'],self.residues['448']))
self.patch(residue_type='DISU', residues=(self.residues['420'],self.residues['482']))
log.verbose()
env = environ()
# Give less weight to all soft-sphere restraints:
env.schedule_scale = physical.values(default=1.0, soft_sphere=0.7)
env.io.atom_files_directory = ['.', '../atom_files']
a = Mymodel(env, alnfile='GBSS1-mult.ali',knowns=('2r4tA','3copA','3cx4A'), sequence='GBSS1')
a.starting_model =1
a.ending_model = 60
# Very thorough VTFM optimization:
a.library_schedule = autosched.slow
a.max_var_iterations = 300
# Thorough MD optimization:
a.md_level = refine.very_slow
# Repeat the whole cycle 2 times and do not stop unless obj.func. > 1E6
a.repeat_optimization = 8
a.max_molpdf = 1e8
a.use_parallel_job(j)
a.make()
error:
'module' object has no attribute 'Mymodel' from <Slave on localhost>
