Jean Didier Pie Marechal wrote: > I am building a model with a specific zinc coordination sphere. I > decided to use a full atom run and this actually improved the overall > quality of the models. I have a problem though. In the structure, > the zinc is chelated by several histidines some by delta others by > epsilon chelating modes. However, the resulting models are always > with the same protonation state (epsilon). This leads to undesired > clashes. How can I stipulate modeller to use a given protonation > state with the charmm force field. Should I use the charmm residue > code in the initial pdb? Or should I define this in the python > script.
Modeller only recognizes one kind of histidine, so if you want a different protonation state you'll have to write a patching residue: http://salilab.org/modeller/FAQ.html#9 and then apply it during your model building by overriding the special_patches method: http://salilab.org/modeller/9v6/manual/node66.html
Ben Webb, Modeller Caretaker