AMBER Archive (2009)

Subject: RE: [AMBER] Copper semiempirical parameters

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jun 11 2009 - 11:09:14 CDT

Hi Jacopo,

> i would like to simulate with the QM/MM a copper atom in a protein.
> Could anybody suggest me where to find the parameters to do it, and the
> best method to simulate the copper in Amber.

Copper is tough to do semi-empirically, hence why there are no parameters
available for it in sander's QMMM. I believe there are parameterizations for
copper in PM6 for example, however, this is not currently supported in AMBER
10, we are in the process of adding it. I also am not sure how well even
that would do.

Your options therefore are two fold.

1) Leave the copper out of the QM region. Is the copper critical to the
catalytic activity? Does it provide electrons / change spin state etc? If it
is purely providing a structural basis for the active site then you could
conceivably leave it in the MM region and still be able to run the
calculations.

2) Use pupil to couple your simulation to an Ab Initio program such as
Gaussian and use a full Ab Initio approach to treat the copper atom. This
will of course be a much much more expensive simulation.

Good luck,
Ross

/\
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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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