I'm having some trouble using the model_patch() command to create a
disulfide bond.
Your first script does the following:
1. Create a topology containing a disulfide bond, and then evaluate the
energy of the initial structure against this topology (the energy will
be high since the bond will be strongly violated, most likely).
2. Throw this structure away and then ask automodel to build a model
without a disulfide bond. ;)
That's probably not what you meant to do.
Your second script is closer, but the method needs to be called
special_patches, not patches; see
http://salilab.org/modeller/9.12/manual/node24.htmlYou should also only call patch(); automodel does all the complete_pdb,
restraints generation, energy calculation itself so there's no need to
do that here.
It returns a KeyError: 'No such residue'. I researched this in the
answer archives and found the suggestion to create a .ini file to
determine the model residue numbers
Unfortunately that suggestion isn't correct. ;) Just remove the :A for
each residue. When you only have a single chain in your model, Modeller
doesn't assign a chain ID.