I have a little problem with Modeller 8v0. Usually it patches disulfide
bonds automatically. But when I try to make model of my protein, it
patches only one disulfide instead of five. When I try to define these
bonds manually (like in FAQ p.3), the procedure stops and says:
What can be the root of problem? Input files are here. The template is a
protein with pdb id 1yi5, slightly minimized in Sybyl. When I use pdb
id 1ux2 as a template, there are no problems, and disulfide bonds are on
their place.
# Homology modelling by the automodel class
from modeller.automodel import * # Load the automodel class
log.verbose() # request verbose output
env = environ() # create a new MODELLER environment to build this model in
# directories for input atom files
env.io.atom_files_directory = './'
a = allhmodel(env,
alnfile = 'align.ali', # alignment filename
knowns = '1yi5_min', # codes of the templates
sequence = 'r1') # code of the target
# Very thorough VTFM optimization:
a.library_schedule = 1
a.max_var_iterations = 300
# Very thorough MD optimization:
a.md_level = refine.very_slow
# Repeat the whole cycle 3-times and do not stop unless obj.func. > 1E6
a.repeat_optimization = 3
a.max_molpdf = 1e6
a.make() # do the actual homology modelling