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)?
>
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Dr Mark J Forster Ph.D.
Principal Scientist
Informatics Laboratory
National Institute for Biological Standards and Control
Blanche Lane, South Mimms,
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Tel +44 (0)1707 654753
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Received on Thu Feb 15 2001 - 02:11:24 PST
