AMBER Archive (2008)

Subject: Re: AMBER: Metal parameter values

From: musa özboyacı (musaozboyaci_at_gmail.com)
Date: Thu Oct 23 2008 - 14:09:35 CDT

I already did it! But the structure I have is basically a protein having a
metal centers. So, I suppose these parameters should be unique for each
structure, right? I mean how accurate the parameters in other systems, can
be for the system of mine?
Thanks for your helps..

Musa

2008/10/23 Bill Ross <ross_at_cgl.ucsf.edu>

> > 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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