From: Aditya Padhi (
Date: Wed May 23 2012 - 22:56:10 CDT

Dear VMD users,
        I want to calculate the "energy or force" exerted between amino
acid residues interacted by Hydrogen bonds throughout a total trajectory
from MD simulation of a protein performed using Amber 10.

(Example: H-bond between Isoleucine17-Asp15, Asp15-Ile46, Ile46-His13 etc,
I want to calculate the H-bond interaction energy between these pair of
residues and hence the net energy).

I searched in the tutorials and literature but could not able to find any
appropriate solutions. If anyone has the idea, please assist me finding the
solution of this problem.

Thanking you,