AMBER Archive (2008)

Subject: Re: AMBER: Nonbonded FE parameter missing in frcmod.

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Sep 11 2008 - 12:19:53 CDT

On Thu, Sep 11, 2008, moitrayee_at_mbu.iisc.ernet.in wrote:
>
> I am trying to simulate a protein having [3fe-4s]+1 as a ligand.

You are going to have to do work on your own here: antechamber does not
support metal ions for automatic generation of force fields.

My suggestion is to look for force fields for fe4s4 clusters, and then see
if you can modify them for the 3fe clusters. Depending on what you are
interested in (i.e. the properties of the cluster itself, or of the protein at
distances far removed from the cluster?) you may need a fair amount of effort
to get things set up.

...dac

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