Re: [AMBER] Parameters for Iron Oxide

From: Maria Nagan <>
Date: Fri, 12 Feb 2021 17:49:07 -0500


You’re correct. They don’t have lib files or frcmod files because that article performed simulations in NWCHEM. You need an article that simulated them in the program Amber not just with protein force field parameters developed by the Amber community. So look for an article that simulated with Amber and the chemistry you want. Google came up with a number of recent articles that probably will be relevant.

Also - FYI Vinícius Cruzeiro has a tutorial with a heme.


> On Feb 11, 2021, at 5:42 AM, Matthew Guberman-Pfeffer <> wrote:
> Dear Amber Community,
> I want to study protein-mineral interactions, where the mineral is specifically one of the common forms of iron oxide. The article J. Phys. Chem. C 2007, 111, 30, 11363–11375 makes it sound as if the Amber force field already has bonded parameters for Fe-hydroxyl interactions (no bonded terms were used for Fe and non-hydroxyl oxygens as these atoms were fixed): "Finally, we made use of the AMBER force field parameters for the iron oxide-cytochrome short-range interactions as well as for the iron oxide-surface hydroxyl interactions.” But, the paper does neither provide a citation nor indicate the atom types that were used, leaving me rather clueless as to what specific parameters were invoked. I’ve tried contacting the authors twice to no avail (the paper is rather old). Can anyone point in the right direction as to what parameters I could use for iron oxide, or if needed, how I would parameterize the needed terms?
> Best regards,
> Matthew Guberman-Pfeffer
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Received on Fri Feb 12 2021 - 15:00:04 PST
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