AMBER Archive (2004)

Subject: Re: AMBER: Antechamber and dummy atoms

From: David A. Case (
Date: Fri Aug 13 2004 - 09:49:49 CDT

On Fri, Aug 13, 2004, Perdita Barran wrote:
> The molecule contains a Zn atom co-ordinated to 3 pyrole like rings. . How
> should I treat this? I have a crystal structure of this and hence can input
> all parameters (particularly those related to Zinc. It seems as if gaff does
> not include the option of a dummy atom, or does it?

No, antechamber doesn't know about dummy atoms, or metals (as you know

> I have used p3 as a substitute which works in so far as I can generate a
> readable prepi file but this not really the right solution.

This sounds like a pretty good solution to me, in the absence any more general
algorithms in antechamber. Sometimes you have to be imaginative, as you have
been here.

> I have Amber7 at present but am upgrading with in the next couple of weeks
> to Amber8.

It is probably good to upgrade, but it won't help the zinc problem mentioned

...good luck...dac

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