Re: [modeller_usage] Histidine protonation state with allhmodel

[Modeller Caretaker <>]

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
-- 
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