Re: AMBER: Simulating transition metals in amber

From: FyD <>
Date: Mon, 24 Oct 2005 10:21:52 +0200

Hi Thomas,

> does anyone have experience with simulations of transition metal
> organic complexes in amber? We are expecially interested in a
> Palladium-complex.

The problem is to have the force field for your UNIT ;-)

> Can someone point me to a good resource on how to set up such a system
> and generate the parameters for it?

I would use R.E.D. to generate RESP or ESP charges:
You have to check if an ECP is needed for the geom. opt. & MEP QM steps. I guess
'yes'. You will also have to define a radius for the palladium (to compute the
MEP; as it is defined for the Sc-Zn elements in R.E.D.-II). If you do need an
ECP, you will also have to modify the R.E.D. source code to add this ECP: you
have to apply the same idea than what has been done for these raddi in
R.E.D.-II. I would be very interested to help setting R.E.D.-II (or better
R.E.D.-III) for your project if you want.

kind regards, Francois

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Received on Mon Oct 24 2005 - 09:53:00 PDT
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