Hi, I am trying to model a protein with certain distance restraints and disulphide bonds. I wonder why restraint does not work when I set disulphide bonds. My script looks like.
--------------------------------------------- from modeller import * from modeller.automodel import * # Load the automodel class import sys
log.verbose() env = environ() env.io.hetatm = True env.schedule_scale = physical.values(default=1.0, soft_sphere=0.7)
# directories for input atom files env.io.atom_files_directory = ['.', '../atom_files']
class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms
# Residues to be an alpha helix: rsr.add(secondary_structure.alpha(self.residue_range('1:', '22:'))) rsr.add(secondary_structure.alpha(self.residue_range('26:', '32:')))
rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['CA:1'], at['CA:269']), mean=4.0, stdev=4.0))
def special_patches(self, aln): # A disulfide between residues X and Y: self.patch(residue_type='DISU', residues=(self.residues['113'], self.residues['117'])) self.patch(residue_type='DISU', residues=(self.residues['125'], self.residues['175'])) self.patch(residue_type='DISU', residues=(self.residues['313'], self.residues['337'])) self.patch(residue_type='DISU', residues=(self.residues['24'],
self.residues['314']))a = MyModel(env, alnfile = 'seq.ali', # alignment filename knowns = ('XYZ','ABC'), # codes of the templates sequence = 'prot', assess_methods=(assess.DOPE, assess.GA341)) # code of the target a.starting_model= 1 # index of the first model a.ending_model = 20 # index of the last model # (determines how many models to calculate)
a.library_schedule = autosched.fast # Very thorough VTFM optimization a.max_var_iterations = 100 a.md_level = refine.fast # Thorough MD optimization a.repeat_optimization = 1 # Repeat the whole cycle 2 times and.. a.max_molpdf = 1e6 # do not stop unless obj.func. > 1E6
#a.use_parallel_job(j) # Use the job for model building a.make() -------------------------------------------------------
If I comment distance restraint seems to work okay. What can be the reason that it does not work with S-S restraints. Moreover, Is there a way to control force constant for harmonic restraints in such cases ?
Best, SM