Hi
well, your question really is about what to simulate for folding and not
as much as the constant pH part.
Constant pH allows to define as titratable one or more residues of your
choice. The rest is simply molecular dynamics. So, if you have evidence
that just the c-terminus changes conformations vs pH (by that I mean the
ISOLATED c-terminus), then you could just simulate that. If on the other
hand the C-terminus changes conformation in the presence of the rest of
the protein, then you probably need the whole thing.
Cheers
Adrian
On 6/1/11 7:25 PM, George Tzotzos wrote:
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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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 - 13:00:03 PDT
