AMBER Archive (2008)

Subject: Re: AMBER: Metal parameter values

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Oct 23 2008 - 13:23:08 CDT

> I have a structure which have Fe and Ni metals inside. As amber does not
> have any Van Der Waals parameters defined for these elements, I need to
> derive these values for the atoms. However I am not sure how I can derive
> (or basically obtain from somewhere) these values. I would be gratefull if
> you help me!

Assuming you are interested in ions, try a google search on
[amber ion parameters], and this reference:

    Ion-Induced Stabilization of the G-DNA Quadruplex: Free Energy Perturbation
    Studies. W.S. Ross and C.C. Hardin
    Journal of the American Chemical Society 116, 6070 (1994).

Bill
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