On 4/22/10 6:57 AM, Davide Pirolli wrote:
I'm a PhD student and I'm using modeller version 9. I'd very glad if you could explain to me which is the solvation model used by modeller in the various steps (in particular in the simulated annealing refinement procedure, CG_minimization, MD etc.)
No solvation model is used. The effect of solvation, like electrostatics, is assumed to be encoded in the structure of your template(s), and thus in the distance restraints derived from those templates.
and the temperatures at which SA is carried out in the high optimization level procedure.
Look at the Python functions defined in modlib/modeller/automodel/refine.py under your Modeller installation directory. They define the temperatures and other parameters for the SA dynamics runs.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage