AMBER Archive (2008)

Subject: Re: AMBER: RE: Force Field Parameterizing

From: David A. Case (
Date: Tue Mar 25 2008 - 10:23:34 CDT

On Mon, Mar 24, 2008, Shultz, Jack wrote:
> I'm looking at the H-Cluster for Fe-Hydrogenase, trying to generate a
> topology file. Xleap does not have bond parameters for Iron. So I tried to
> generate the parameters using antechamber and got these error messages. In
> order to find parameters should I harvest from literature or is there
> another way to generate the parameters I'm seeking.
> I understand these transition metals present theoretical problems with their
> complicated orbitals. Is Amber well suited for this type of problem?

Not really. If you just want to have the metal cluster "sit there" (not doing
any chemistry), then you can, with some effort, define a topology for it.

Antechamber cannot handle metals, just organic molecules, so you have to do
things here by hand.


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