AMBER Archive (2008)

Subject: Re: AMBER: reg-antichamber run

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Dec 10 2008 - 17:14:31 CST

On Wed, Dec 10, 2008, balaji nagarajan wrote:
>
> I tried in building the parameter and topology for
> cobalt(III) hexammine (3+)
> using antichamber .

Antechamber deals with organic molecules: it doesn't know how to deal with
metal ions.

On the other hand, there are existing examples of cobalt-hexamine simulations
that can probably be used to get you started, e.g.:

%A T.E. Cheatham, III
%A P.A. Kollman
%T Insights into the stabilization of A-DNA by specific ion association:
spontaneous B-DNA to A-DNA transitions observed in molecular dynamics
simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III)
%J Structure
%V 5
%P 1297-1311
%D 1997

...dac

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