Dear Adrian,
Thank you for the assistance. I have chosen
protonation states of the residues (at pH 1, 3, 5 and 9) with the help of
H++ sever which is recommended by AMBER. So will it be giving the same
results in comparison to constant pH simulation.
On Sat, Jun 26, 2010 at 8:24 AM, Adrian Roitberg <roitberg.qtp.ufl.edu>wrote:
> 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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>
--
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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Received on Sat Jun 26 2010 - 06:00:03 PDT
