[Chimera-users] Hydrogen bond energy calculation

Elaine Meng meng at cgl.ucsf.edu
Thu May 24 08:20:06 PDT 2012

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.
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.

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