Re: [AMBER] Magnesium ion and MMPBSA/GBSA

From: David A Case <>
Date: Mon, 12 Dec 2016 11:34:10 -0500

On Mon, Dec 12, 2016, Francesco Gentile wrote:

> I am running free energy calculations on a series of protein-ligand
> complexes. The ligands are all interacting with a magnesium ion in the
> active site of the enzyme. How should I treat the magnesium ion (part of
> the receptor, the ligand or what else?)?

If the magnesium ion is present in the absence of ligand, it is then really a
part of the "receptor". If not, mmpbsa is not going to help you much.

These metal-ion dependent events are really outside the expected purview of
the mm-pbsa approach: the first shell of waters around the ion are really
important, and cannot generally be replaced by an implicit solvent. You are
likely to find that your results depend very strongly on the radius you assign
to Mg, and there is no "correct" value to use.


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Received on Mon Dec 12 2016 - 09:00:02 PST
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