Re: AMBER: molecular dynamics simulation of protein containing Mg2+ cation

From: David A. Case <>
Date: Sun, 3 Jul 2005 16:34:14 -0700

On Fri, Jul 01, 2005, Ye Mei wrote:
> I am studying HIV-1 integrase, which contains a Mg2+ cation. Both D64 and
> D116 coordinate to this Mg2+ cation, together with water molecules and
> sometimes also with a ligand.
> This coordination will strongly effect the charge distribution among Mg2+,
> D64, D116 and other coordinated molecules. I used the default FF03
> parameters for all these residues, but it gave a very strong interaction
> between Mg2+ and a neutral ligand, like -150 Kcal/mol or even more. The
> ligand coordinate to Mg2+ with only 2 oxygen atoms, so -150 Kcal/mol, which
> mainly comes from coulomb interaction, is quite unreasonable. If we consider
> the charge redistribution among all these residues, the interaction should
> decrease.

There are a number of simulations in the literative on HIV integrase, and you
might look at what has been done there. One other example of Mg coordination
is in the following papers:

%A H. Gohlke
%A C. Kiel
%A D.A. Case
%T Insights into Protein-Protein Binding by Binding Free Energy Calculation
and Free Energy Decomposition for the Ras-Raf and Ras-RalGDS Complexes
%J J. Mol. Biol.
%V 330
%P 891-913
%D 2003

%A H. Gohlke
%A D.A. Case
%T Converging Free Energy Estimates: MM-PB(GB)SA Studies on the
Protein-Protein Complex Ras-Raf
%J J. Comput. Chem.
%V 25
%P 238-250
%D 2004

But, as you point out, there is no simple way to handle divalent ions in
(current) molecular mechanics force fields that is fully satisfactory.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Mon Jul 04 2005 - 00:53:01 PDT
Custom Search