AMBER Archive (2006)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Jun 30 2006 - 03:54:28 CDT

To add a Caveat to Kennie's post.

You will also need to add support for d-orbitals to the QM/MM code including
the analytical gradients (not pretty). Work is currently underway to do this
and at that point iron parameters will be added. At present you cannot treat
iron with Amber 9's built in QMMM code. I think divcon may support
d-orbitals (Kennie can comment more on this) in which case you could try
adding the parameters to this and then set idc=1 for the QM calculation in
sander. This will prevent you from using PME, GB etc though.

Note: I also would be skecptical, even with d-orbital support and a good
parameter set, of how semi-empirical methods would for iron compounds,
especially highly delocalised systems such as heme's.

All the best
Ross

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Ken Merz
> Sent: Thursday, June 29, 2006 12:55
> To: amber_at_scripps.edu
> Cc: Kenneth Ayers; SETH ALLEN HAYIK; Bryan Op't Holt; Kevin Riley
> Subject: Re: AMBER: Having trouble getting Iron parameters for QM/MM
>
> 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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