Dear nicholus
It all of course depends on your guess at the constant protonation states.
For instance, if you are simulating a protein at pH=10, then keeping the
glu and asp residues as unprotonated if a very good bet. In that case,
doing a constant protonation MD (with unprotonated asp/glu) and running
a constant pH MD should give you the same sampling of conformational space.
But, if you are simulating at ph=4, then, since the pka of glu and asp
is somewhere around 4 most of the time, there is NO SINGLE constant
protonation state that can accurately reflect the correct physics of the
system.
On 6/26/10 2:19 PM, nicholus bhattacharjee wrote:
> Dear community,
> As we know there are two ways of doing
> simulation of proteins in AMBER: constant protonation and constant pH. My
> query is that will the trajectories be of vast difference when we apply
> this two methods in the same protein? Or will the conformation at different
> time steps remain similar with marginal deviations? Thank you in advance.
>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project
Department of Chemistry
Senior Editor. Journal of Physical Chemistry
American Chemical Society
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
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Received on Sat Jun 26 2010 - 05:30:04 PDT
