Re: [AMBER] About the Mg charge in AMBER FF

From: Jacopo Sgrignani <sgrigna.gmail.com>
Date: Fri, 4 Oct 2013 12:01:43 +0200

Dear George
there are several approaches to simulate Mg2+ in proteins.
In my experience using a simple 2+ charge can produce strong changes
in the Mg2+ coordination sphere.
Also using a "arbitrary" reduction of 0.5 of the charge is not a good idea.

One recipe was proposed in Dal Peraro et. al. J Struct. Biology,
2007, 3, 444. It is based on charge corrections derived using Bader
Atoms in Molecule approach.
Another smart way is using the dummy cation approach developed by
Warshel and coworkers (Oelschlaeger, P.; Klahn, M.; Beard, W. A.;
Wilson, S. H.; Warshel, A. J. Mol. Biol. 2007, 366, 687 701).
I compared this last approach with the geometries sampled in
QM(DFT)/MM simulations (Sgrignani and Magistrato J. Phys. Chem B.
2012) and it seems to work well.
Notably the dummy cation approach does not require any additional
calculations, you only need libraries for amber.

Regards

Jacopo



2013/10/4, George Patargias <gpat.bioacademy.gr>:
> Hello
>
> Sorry if this is trivial. Is there an issue with the +2 charge of Mg in
> AMBER FF or in other FFs? I mean, is there evidence from simulations that
> the use of +2 value will cause artifacts such as too strong interactions
> between Mg and negatively charged residues Asp, Glu?
>
> If this is the case would an ad hoc solution like the reduction of Mg
> charge to, say, +1.5 have any point?
>
> Many thanks in advance for any clue on this.
>
> Best wishes
> George
>
>
> Dr. George Patargias
> Postdoctoral Researcher
> Biomedical Research Foundation
> Academy of Athens
> 4, Soranou Ephessiou
> 115 27
> Athens
> Greece
>
> Office: +302106597568
>
>
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>

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Received on Fri Oct 04 2013 - 03:30:04 PDT
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