AMBER: Antechamber and dummy atoms

From: Perdita Barran <>
Date: Fri, 13 Aug 2004 14:03:44 +0100

Dear Amber Community,
        I am trying to use antechamber to prepare an inorganic molecule for
minimisation etc.

 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?

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.

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

All help most gratefully received

Perdita Barran
Dr. Perdita Barran
EPSRC Advanced Research Fellow
School of Chemistry
The University of Edinburgh
Joseph Black Building
The King's Buildings
West Mains Road
Edinburgh EH9 3JJ

t: +44 (0) 131 650 7533 (office)
t: +44 (0) 131 651 3037 (lab)
f: +44 (0) 131 650 7533

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Received on Fri Aug 13 2004 - 14:53:01 PDT
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