Having only browesd through the papaer very briefly, I can't see how the
protonation state was chosen. The modelling part of the paper wasn't
that informative. There is a web service called H++ that can make pKa
estimates for titrating sites. Not sure how accurate it is though. It
uses continuum electrostatics that may not be accurate enough for pKa
estimates (see e.g. reviews by Warshel from 1991 and 2006). I've never
used H++ myself, only heard about it.
Erik
Monisha Hajra skrev 2011-03-29 17.31:
Thanks Justin. I haven't find any such tutorial or exact relevant
research paper. Find some paper though
(http://peds.oxfordjournals.org/content/16/12/1017.full.pdf+html ),
not sure how they have done.
On Tue, Mar 29, 2011 at 8:51 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Monisha Hajra wrote:
Friends,
Need a Gromacs tutorial to find effect of pH on catalytic
side. Any help?
There probably isn't one. If it isn't at
http://www.gromacs.org/Documentation/Tutorials or you can't find
it with Google, then it doesn't exist.
You'll probably want to look into the ability of pdb2gmx to alter
side chain protonation state, and otherwise base your procedures
on published literature. You may need to use QM/MM rather than
vanilla MD for this type of process, depending on your system and
your goals.
-Justin
Regards
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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