Re: SMD with different pH

From: Brian Bennion (
Date: Fri Mar 05 2004 - 10:16:09 CST

Hello Volodya
You have just struck on one of the most thought about problems in
classical computational chemistry. As long as you are in the classical
regime you will never know what the solution pH is, because
water never forms its equilibrium with OH- and H30+.
Having said that, some people will make a very gross approximation and
assign pH by changing the protonation state of various amino acids. But
unless you have titration data from NMR experiments you still don't know
which histidines are protonated in your case.

A semi empirical package called COSMO-RS is as about as close you can get
without going full ab initio to determine protonation states.

On Fri, 5 Mar 2004, Volodymyr Nechiporuk-Zloy wrote:

> Dear NAMD users,
> I want to model the unbinding of a peptide from a protein with
> different pH (6.0-7.5). How can I perform this? How can I note the pH of
> solution in the model. I want to use namd2 (SMD). I can also use other
> packages of programs. Any suggestions will be lelpfully.
> Sincerely your,
> Volodya

**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **

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