On Sat, Jun 26, 2010 at 8:50 AM, nicholus bhattacharjee <
nicholusbhattacharjee.gmail.com> wrote:
> 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
>
For pH 1, the H++ server will probably do a good job. For pH 3 and 5, the
pKa of carboxylate residues (Asp and Glu) is around 4 and 4.4, respectively,
so these residues may need to be treated with constant pH to reproduce the
correct ensemble of protonation states. pH 9 may affect the tyrosine and
lysine residues. Also bear in mind that pKa and conformation are coupled,
so basing your pKa calculations on a single structure may not be at all
correct.
H++ sever which is recommended by AMBER. So will it be giving the same
> results in comparison to constant pH simulation.
>
Not always, since H++ uses a single structure, I believe. If the pKa
changes as new conformations are explored, then H++ may be quite wrong. The
only way to know for sure is to run both.
Good luck!
Jason
>
> 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Nicholus Bhattacharjee
> PhD Scholar
> Department of Chemistry
> University of Delhi
> Delhi-110007 (INDIA)
> Phone: 9873098743(M)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Jun 26 2010 - 07:00:03 PDT
