Re: AMBER: Representation of cations in MD

From: David A. Case <>
Date: Fri, 20 May 2005 08:16:15 -0700

On Fri, May 20, 2005, Thomas Steinbrecher wrote:
> I seem to recall that there is a paper that discussed representing a
> cation of charge +2 (magnesium or zinc?) in an MD simulation as one big
> particle including its inner solvation shell. The study was concerned with
> the binding of the cation to a biomolecule.

Sounds like this one:

%A V. Tsui
%A D.A. Case
%T Calculations of the Absolute Free Energies of Binding between RNA and Metal
%Ions Using Molecular Dynamics Simulations and Continuum Electrostatics
%J J. Phys. Chem. B
%V 105
%P 11314-11325
%D 2001

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri May 20 2005 - 16:53:01 PDT
Custom Search