AMBER Archive (2005)

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

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Thu Dec 01 2005 - 13:26:11 CST

I don't know the answer but I would worry about whether the
force field itself works for divalent cations without polarizability.
There might be more errors than just the solvation model.

mingche Pan wrote:

> Dear AMBER users,
>
> 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.
>
> I would appreciate if someone can explain a bit more on this issue,
> and suggest a method I can use for this situation.
>
> Thanks a lot!
>
> Mingche Pan
>
>
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