Re: [AMBER] Magnesium ion and MMPBSA/GBSA

From: Ray Luo <>
Date: Mon, 12 Dec 2016 08:52:48 -0800

Hi Francesco,

We met something similar in a recent study for the human purinergic
platelet receptor (J. Phys. Chem. B, 2016, 120 (48), pp 12293–12304).
Indeed, different approaches used to model Mg++ do noticeably impact
the agreement with experimental data.

All the best,
Ray Luo, Ph.D.
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Sun, Dec 11, 2016 at 11:44 PM, Francesco Gentile
<> wrote:
> Hello,
> 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?)? Also, does someone has experience
> with this kind of situation and maybe can help me in setting up correctly
> the calculation? Thanks in advance
> --
> Francesco Gentile
> PhD Student, Biophysics
> CCIS 3-215, Department of Physics
> 7-112, Li Ka Shing Centre for Health Research Innovation
> University of Alberta, Edmonton, AB T6G 2E1
> Canada
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Received on Mon Dec 12 2016 - 09:00:03 PST
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