[gmx-users] Effect of pH on catalytic side

[Monisha Hajra]

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.
>
> 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 <jalemkul at 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 | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>
>
>
> --
> -----------------------------------------------
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
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