VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Jan 18 2007 - 18:23:24 CST

Hi Amit,
this depends on what you mean by hbond energy. If you're using a modern
CHARMM forcefield, there *is* no hbond energy -- they're implicit in the
electrostatic and VDW interactions. You can use namdenergy to get the
nonbond interactions between these residues, or write your own script to
take the coordinates in vmd and run them through an arbitrary energy
function over the trajectory.

Peter

amit dong wrote:
>
> Hi,
> I need to calculate H-bond energy between a pair of residues for the
> whole trajectory. I was wondering if there is any quick way of doing it.
> Thanks
> Amit