Thank you Adrian. It's clearer to me now.
George
On Jun 1, 2011, at 9:49 PM, Adrian Roitberg wrote:
> 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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>>
>>
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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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Jun 01 2011 - 13:30:04 PDT
