On 1/30/14 4:58 PM, Roland Rivera wrote: > 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.html You 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.
Ben Webb, Modeller Caretaker