AMBER Archive (2006)

Subject: Re: AMBER: Ti calculations in dmso solvent

From: David A. Case (
Date: Thu Feb 23 2006 - 12:01:26 CST

On Thu, Feb 23, 2006, David Mobley wrote:

> Usually to use PME you require that the
> system be neutral; it seems difficult to maintain this if the ligand whose
> charges are being turned off is charged. The problem isn't as apparent with
> cutoff electrostatics, but it's not obvious to me that this means that there
> will be no problem. Perhaps someone else can comment on this?

This subject has been carefully explored here:

%A T. Darden
%A D. Pearlman
%A L.G. Pedersen
%T Ionic charging free energies: Spherical versus periodic boundary
%J J. Chem. Phys.
%V 109
%P 10921-10935
%D 1998

This paper argues that you can do standard charging free energy calculations
in a straightforward fashion using PME. There is no requirement in PME that
the system be neutral...indeed, it can't be at both ends of a charge change. As
my comment, I don't see how using cutoff electrostatics would lead to
consistent or correct results.

For a recent application of free energy calculations where the charge is
changing, you might look here (among other places!):

%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


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