[gmx-users] Effect of pH on catalytic side

[Monisha Hajra]

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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