look at manual (Amber 11 only!) for constant pH simulations.
There is no tutorial yet, but the test cases should guide you reasonably
well. Now, this is advanced stuff, so you need to feel really
comfortable with regular sander and MD simulations before trying
constant pH.
Adrian
On 6/1/11 6:32 PM, George Tzotzos wrote:
> I'm dealing with a protein whose 12-residue carboxy end is an unstructured random coil at pH 7. This terminal end undergoes a transition to helical form at pH 4.5
>
> I was thinking of following an approach similar to tutorial 3 to predict the folding of the terminal oligopeptide, however I don't have any clear ideas on how to factor in pH effects.
>
> I'd appreciate any ideas on this.
>
> Regards
>
> George
>
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--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project, Department of Chemistry
University of Florida
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
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Received on Wed Jun 01 2011 - 10:00:04 PDT
