Re: AMBER: global pH variation in AMBER.

From: David A. Case <>
Date: Tue, 8 Mar 2005 11:38:30 -0800

On Tue, Mar 08, 2005, Osman Gani wrote:

> I can make temperature variations, no doubt. And I can make different
> ionization scenarios of these 3 residues in AMBER. But how can I correlate
> different ionization scenarios of these 3 residues with global(!) pH values
> as done in experiments?

> So that, finally i can say that at specific ionization scenario (that
> correspponds to a specific pH) i get a specific amount of free energy.

There is a "consant pH" facility (see the manual) that gets close to what you
are asking for; this only works for implicit solvation. You could also
calculate pKa's of the individual sidechains (in either implicit or explict
solvent) and use that to get an absolute scale. For an example, see:

%A T. Simonson
%A J. Carlsson
%A D.A. Case
%T Proton binding to proteins: pKa calculations with explicit and implicit
%solvent models
%J J. Am. Chem. Soc.
%V 126
%P 4167-4180
%D 2004

....good luck...dac

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Received on Tue Mar 08 2005 - 19:53:03 PST
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