[gmx-users] Effect of pH on catalytic side
hajra.monisha at gmail.com
Tue Mar 29 18:02:08 CEST 2011
Thanks Erik for the information.
On Tue, Mar 29, 2011 at 9:11 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> 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> 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 | (540) 231-9080
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> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: +46 18 471 4537 fax: +46 18 511 755erikm at xray.bmc.uu.se http://folding.bmc.uu.se/
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