Hi Brett,
it's hard to help from the information that you give us. can you tell us
your goals for running the MD? it sounds like the crystal structure may
have ramachandran outliers. what is the quality of the crystal structure,
especially in those regions? Do you think it is poor quality, and are
expecting the MD to fix it? or is the crystal structure reliable and you
are wondering something else? we don't know what force field or solvent
model you're using, or the conditions in the experiment that you are trying
to match.
if you are asking about a poor quality initial structure and why it does
not improve with MD, there are articles out there about using MD for
structure refinement, those might help you to find good protocols and also
understand the challenges in achieving success. A lot starts with
evaluating the quality of the crystal structure beyond # outliers.
On Sun, Sep 20, 2015 at 7:49 AM, Brett <brettliu123.163.com> wrote:
> Dear All,
>
>
> I have a protein structure with 82.9% Ramachandran favoured (high
> percentage of Ramachandran allowable and outlier). With tough
> equilibration, I have run a 30 ns production MD of that protein. But I find
> the PDB at 30 ns is still only with 83.84% Ramachandran favoured (still
> high percentage of Ramachandran allowable and outlier).
>
>
> Will you please explain why the MD process did not lead to the ideal
> protein state, i.e., with more than 99% Ramachandran favoured?
>
>
> Best regards.
>
>
> Brett
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Received on Sun Sep 20 2015 - 05:30:04 PDT
