Re: [AMBER] MMPBSA and explicit ions: what should I do?

From: David A Case <>
Date: Thu, 1 Mar 2012 08:11:42 -0500

On Thu, Mar 01, 2012, wrote:

> I am performing some simulations in order to compute the binding free
> energy of hyaluronic acid and BMP2 protein.
> I would like to use MMPBSA approach in order to obtain the desidered value.
> However, in the simulation box I had to add 14 Cl- ions in order to
> assure electroneutrality.
> Since I have explicit ions, how can I consider them in MMPBSA?
> Can I remove them and consider them in implicit way through ionic strenght?

This is the way that the MM-PBSA model was originally intended to be used
(i.e. removing the ions and setting the ionic strength in the GB/MB model).
See, for example, the very first paper on this subject:

%A J. Srinivasan
%A T.E. Cheatham, III
%A P. Cieplak
%A P. Kollman
%A D.A. Case
%T Continuum Solvent Studies of the Stability of DNA, RNA, and
Phosphoramidate--DNA Helices
%J J. Am. Chem. Soc.
%V 120
%P 9401-9409
%D 1998

It's possible to imagine other ways of proceeding, but that would be a
significant research topic: one would need GB/PB parameters for explicit ions;
one would need to check that the snapshots chosen are fully sampling the ion
positions (which in many cases will be much more difficult than sampling the
solute conformational space); one would need to show that the procedure
actually works on some test cases where one knows what the correct behavior
should be; finally, one should find a significant advantage compared to the
standard behavior, since the latter is much cheaper and simpler.


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Received on Thu Mar 01 2012 - 05:30:02 PST
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