AMBER Archive (2006)

Subject: Re: AMBER: Having trouble getting Iron parameters for QM/MM

From: Ken Merz (merz_at_qtp.ufl.edu)
Date: Thu Jun 29 2006 - 14:54:45 CDT

Hi,
  For Fe you could take a look at the following:

http://www3.interscience.wiley.com/cgi-bin/abstract/112657117/ABSTRACT

I have no idea how good they are because they are hot off the press
as it were, but they are for PM3. You will need to build them into
the QM part of the QM/MM code.

Good luck.

Kennie

On Jun 29, 2006, at 3:23 PM, zachary hartman wrote:

> We're running AMBER 9 on SGI Fuels, and we've exhausted as many
> methods as we could find, but none listed iron as a compatible atom
> type for the calculation of QM/MM through sander.
>
> Our iron is the central atom of a heme in a +3 oxidation state. Is
> anybody able to give us parameters and/or advice for where to place
> these parameters?
>
> Or if you could tell us how to calculate the parameters for
> ourselves, that would be wonderful, also!
>
>
> Thank you very much,
>
> Zach Hartman
>
>
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Professor Kenneth M. Merz, Jr.
Department of Chemistry
Quantum Theory Project
2328 New Physics Building
PO Box 118435
University of Florida
Gainesville, Florida 32611-8435

e-mail: merz_at_qtp.ufl.edu
http://www.qtp.ufl.edu/~merz

Phone: 352-392-6973
FAX: 352-392-8722
Cell: 814-360-0376

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