Re: AMBER: Metals with Amber

From: Bill Ross <>
Date: Fri, 28 Oct 2005 13:56:50 -0700 (PDT)

> We are currently interested in doing some MD simulations to study
> interactions between the proteins and different metal ions, such as Zn,
> Cd or As (identification of possible binding sites?). I would really
> appreciate any feedback regarding the current standing of computational
> approaches for the modeling of protein interactions with the different
> metals ions. Basically, we are wondering how well the current Amber
> force field reproduces such interactions?

I believe that multivalent ions are considered technically
beyond the point charge approximation, not sure whether
polarization would solve that.

Note that parameters (vdw) derived for ion-water interactions,
such as Aqvist and I believe all others in amber ff files do
not apply for ions in complex with other types of molecule,
due to the large vdw assigned to water O in tip3 and spc water
potentials. Discussion of this difference and a formula for
deriving monovalent cation vdw params can be found in:

        Ion-Induced Stabilization of the G-DNA Quadruplex: Free
        Energy Perturbation Studies. W.S. Ross and C.C. Hardin
        Journal of the American Chemical Society 116, 6070 (1994).

> And would the differences
> between two positively charged cations: like Zn2+ or Cd2+ be well
> represented? Or will they be treated as similar entities by Amber?

Vdw is the only thing that will change in the current ff, so in a
sense you are looking at the Born approximation.

There has been work on an ion/protein ff based on xtal studies I believe,
likely referenced in our paper. It would be nontrivial to add to amber
but potentially worthwhile for studies such as you propose.

A google search on [ion protein "force field"] yields some interesting

Bill Ross
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Received on Fri Oct 28 2005 - 22:53:01 PDT
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