AMBER Archive (2006)

Subject: AMBER:

From: Ken Merz (merz_at_qtp.ufl.edu)
Date: Sat Jul 29 2006 - 10:28:53 CDT

Hi,

  Yes, you will need to build parameters for the Zn-S bond and, no, I
do not believe that they are in the parm99.dat file. Someone correct
me if I am wrong. Ulf Ryde has worked on systems with Cys-Zn bonds,
so you could start with his work from a few years ago. There is an
ASAP article on an MD simulation of SOD which has Zn-Cys bonds from a
group in Oporto, Portugal. Lim has created some more advanced models,
but this would require work on your part to build it into AMBER I
believe. Others have created ff's for Zn systems - you could look at
some of Lucia Banci's work as well as work we have done in this area.
Others have modeled systems like these without bonds: see for example
Roland Stote's work with Martin Karplus (Proteins 1995, 23, 12-31 I
believe) as well as that of Vedani (see Hoops et al 1991 JACS paper).
Other have contributed to this research area as well, so the names
listed above are just a sampling of what is out there in the
literature. Good luck.

Kennie

Professor Kenneth M. Merz, Jr.
Department of Chemistry
Quantum Theory Project
2328 New Physics Building
PO Box 118435
University of Florida
Gainesville, Florida 32611-8435

e-mail: merz_at_qtp.ufl.edu
http://www.qtp.ufl.edu/~merz

Phone: 352-392-6973
FAX: 352-392-8722
Cell: 814-360-0376

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