AMBER Archive (2007)

Subject: Re: AMBER: Should we just vary one parameter at a time only for PMF calculations?

From: David A. Case (case_at_scripps.edu)
Date: Fri Jun 08 2007 - 10:55:12 CDT

On Thu, Jun 07, 2007, Catein Catherine wrote:
>
> I could like to do the PMF calculation by varying the distance between the
> drug and the receptor.
>
> However, by varying the distance, the angles between the drug and receptors
> always changed too? Is it expected? Is it necessary to fix the angles
> between them?

Amber doesn't have any simple way to do this, and it is not clear (to me!)
how such a result would be interpreted. You might want to look at the
following paper for an example of computing a ligand-protein pmf; maybe it
will help clarify some of the issues involved:

%A O. Guvench
%A D.J. Price
%A C.L. Brooks, III
%T Receptor rigidity and ligand mobility in trypsin-ligand complexes
%J Proteins
%V 58
%P 407-417
%D 2004

...regards...dac

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