Re: AMBER: questions about run MD at different pH

From: David A. Case <>
Date: Tue, 4 Mar 2008 17:59:49 -0800

On Tue, Mar 04, 2008, Kailee wrote:
> So, in normal MD simulations, there is no 'pH' such parameter, although the
> protonation states of amino acids are assigned according to pH, which can be
> done beforehand? and can you give a few examples of those unphysical fixed
> set of protonation states please?

*Any* fixed protonation state is to some extent unphysical: a carboxylic acid
side chain really exists in solution as an equilibrium mixture of protonated
and unprotonated forms (ditto for other acids and bases).

> So if the metal ions
> and their neighbouring amino acids have fixed protonation states at
> different pHs, then the constant pH calculations method should be an easier
> choice to compare results at different pHs?

This means that you don't have to do anything special to run a constant pH
simulation, just because of your extra residues. Nothing involving pH is
"easy", however, and all of it is kind of at the "bleeding edge", out beyond
where there are reasonably standard protocols. No matter what course you
take, you should expect problems. Be sure to study carefully the "constant
pH" literature, and see if it looks like it would satisfy your needs. Start
with simple things -- be sure you understand how to work with a single
titrating site before moving on to harder problems.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Mar 05 2008 - 06:07:39 PST
Custom Search