[gmx-users] Effect of pH on catalytic side
erikm at xray.bmc.uu.se
Tue Mar 29 17:41:12 CEST 2011
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.
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 <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> Monisha Hajra wrote:
> 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 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
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Erik Marklund, PhD student
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