Date: Thu, 15 Feb 2001 10:11:24 +0000
From: Mark Forster
Subject: Re: how to handle a metal ion

Dear Jake

These papers describe Zn parameters in AMBER (and also in other forcefields such
as Charmm).

1) Structural differences of matrix metalloproteinases. Homology modeling and
energy minimization of
enzyme-substrate complexes
Terp GE, Christensen IT, Jorgensen FS
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
17: (6) 933-946 JUN 2000

2) ZINC-BINDING IN PROTEINS AND SOLUTION - A SIMPLE BUT ACCURATE NONBONDED
REPRESENTATION
STOTE RH, KARPLUS M
PROTEINS-STRUCTURE FUNCTION AND GENETICS
23: (1) 12-31 SEP 1995

Note that Zn is sometimes treated as covalently bonded to the coordinating
species
rather than as a free ion. If you find a good set of parameters please let me
know
what they are.

Hope this helps.

Mark F

Jake Isaacs wrote:

> The protein I wish to study has a zinc atom chelated by Cys, His, and Asp
> (both O's). What might a reasonable partial charge be for the zinc atom and
> what, if any, changes need to be made to the charges of the ligand atoms?
> What other sort of parameters must I assign the zinc atom for sander to be
> able to use it (vdw radius?), since it won't be participating in any
> covalent bonds?
>
> These (and previous) questions are for "quick and dirty" minimizations and
> short MD runs, so a full quantum mechanical treatment might not be worth the
> effort. Would harmonic restraints between the ligand atoms and the zinc be
> the best way to keep the atom in place, or should it maintain itself through
> non-bonded interactions with it's ligands? Also, in reference to previous
> questions about small molecule paramterization, would assigning atom types
> and estimated partial charges (from similar atoms in amino acids and
> nucleotides) be sufficient for sander to handle a molecule containing only
> C, H, O, and P (again, just for "quick and dirty" applications)?
>