AMBER Archive (2004)

Subject: AMBER: Antechamber and dummy atoms

From: Perdita Barran (perdita.barran_at_ed.ac.uk)
Date: Fri Aug 13 2004 - 08:03:44 CDT

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
e: perdita.barran_at_ed.ac.uk
w: http://www.chem.ed.ac.uk/staff/barran.html

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