Dear All, 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. Thanks for any help
Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es
----- Missatge original ----- De: modeller_usage-request@salilab.org Data: Divendres, Febrer 20, 2009 4:02 pm Assumpte: modeller_usage Digest, Vol 8, Issue 12
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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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Jean Didier Pie Marechal -
Modeller Caretaker