Re: AMBER: Antechamber and dummy atoms

From: Oliver Hucke <>
Date: Fri, 13 Aug 2004 10:55:57 -0700


I am also working with zinc bound to organic molecules (as protein
inhibitors in my case). I found the papers from the group of Ken Merz
(e.g. Biochem. v.41 p. 6615, JACS v. 113 p.8262 - the latter is THE
paper on the method I would say) very helpful. His group has lots of
experience with simulations of zinc containing systems with the amber
So, to get reasonable charges reflecting the charge transfer from the
zinc to the ligands I am doing a resp charge fit to a model system with
QM-optimized geometry. In your case the model system could e.g. consist
of the zinc and the pyrrole rings. The resp charges for each of the
complete ligands without zinc are obtained with the same procedure in
separate calculations. After this you need to transfer the charges from
the model system and correct the charges of the atoms connecting to the
pyrroles in the complete system to get the overall correct charge for
the complete system with zinc. After the correction each overall ligand
charge should be the charge shifted to the corresponding pyrrole by
charge transfer. In other words, the sum of the remaining zinc charge
(usually ~+1e) and the charges of the ligands should equal +2 (I presume
neutral ligands and Zn2+).
The prepin files for the ligands can be prepared with antechamber (check
for correct atom types!).
The force field parameters involving the zinc system can either be
obtained following e.g. the procedure described in Biochem. v.41 p. 6615
or, if appropriate, you can simply use published parameters.

Best regards,

Perdita Barran wrote:
> 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:
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Oliver Hucke, Dr.
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Received on Fri Aug 13 2004 - 19:53:00 PDT
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