[gmx-users] Effect of pH on catalytic side

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 29 17:21:31 CEST 2011

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.


> Regards


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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