how to handle a metal ion

From: Jake Isaacs <>
Date: Wed 14 Feb 2001 10:43:14 -0500

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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Received on Wed Feb 14 2001 - 07:43:14 PST
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