AMBER Archive (2005)

Subject: Re: AMBER: Mg2+ issues of using MM-PB/GBSA

From: David A. Case (case_at_scripps.edu)
Date: Thu Dec 01 2005 - 13:47:20 CST

On Thu, Dec 01, 2005, mingche Pan wrote:
>
> I wonder whether I can use MM-PB/GBSA method to calculate the binding free
> energy in the case of Mg2+ directly involving in the ligand binding. The
> initial tests showed that the energy difference calculated by different GB
> methods is up to ~80 kcal/mol, and the difference between GB and PB models
> is also quite large, over 50 kcal/mol. In addition, different Born radii
> of Mg2+ (from 0.99 ?C 1.45) also seem giving various energies, ranging
> from -10 to -130 kcal/mol.

Doing this would represent a real research problem; as your e-mail points out,
you could pretty much get any value you want with minor changes in the
procedure. It's not clear that this will ever work, but it definitely needs
calibration and exploration first.

...dac

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