AMBER Archive (2008)

Subject: Re: AMBER: MD at a given pH

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sat Sep 27 2008 - 06:53:56 CDT

On Fri, Sep 26, 2008, Beale, John wrote:

> I want to do MD on a solvated protein at particular pH values. How can I
> adjust the pH of the system?

About all you can do with current codes is to estimate the pKa values of the
various residues in your structure, and assign (constant) protonation states
based on those estimates. If you don't know the structure of your peptide, or
if it adopts a variety of conformations) you may have to rely on "standard"
pKa values for the various residues.

In the long run, we plan to investigate ways to carry out "constant pH"
simulations in explicit solvent, but that is still a research topic for
future work.

...dac

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