Hi Aditya, Chimera calculates possible H-bonds, but it does not calculate their energies, sorry. Chimera H-bond detection is a yes-or-no decision using geometric (distance and angle) cutoffs. You would have to use some other program to estimate H-bond interaction energies. Regards, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 23, 2012, at 8:57 PM, Aditya Padhi wrote:
Dear Chimera 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, Regards Aditya.