Adrian,
Thanks for this. One related question. Does one perform a constant pH simulation on the protein tail fragment or on the whole protein.
Cheers
George
On Jun 1, 2011, at 6:36 PM, Adrian Roitberg wrote:
> 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 - 10:30:05 PDT
