Re: Metal Ion and Protein binding

From: LEWYN LI (
Date: Thu Oct 13 2005 - 13:38:07 CDT


         NAMD can study ion-protein interactions, if the interactions can
be adequately modelled as electrostatic (+ vdw + etc., if necessary), or
as a covalent bond (e.g. the heme-CO bond in myoglobin).

         One complication is that the charge of the ion may be hard to get.
It is also a bit of a challenge to get values for ion-protein bond

         If you believe that the ion-protein interaction CANNOT be
described by classical electrostatics or as a covalent bond, then you
might wish to explore quantum mechanical packages such as Gaussians.
Quantum calculations usually take much longer than NAMD, though.

         Hope this helps.


On Thu, 13 Oct 2005, Gaurav Sharma wrote:

> Hi All,
> I would like to study the mechanism of metal ion binding to proteins using MD
> simulations. To my understanding NAMD is not capable of simulating such
> reactions since it cannot account for the breaking or formation of bonds.
> Can someone suggest any other software/tool through which I can simulate such
> a system.
> Thanks for your help.
> Gaurav
> --
> Gaurav Sharma
> Computational BioNano Robotics Lab
> Northeastern University
> Boston, MA - 02115
> Tel: 617-373-2970

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