[Chimera-users] MD trajectory hbond analysis

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 13 09:13:10 PDT 2010

Hi George,
There is a FindHBond tool and findhbond command -- when you are showing a trajectory in the MD Movie tool (could be from Amber or any of several other programs), you can use the "per-frame script" feature in that tool to run the calculation at each step and save the results.

Please see these previous posts for more details on doing that:

It sounds like you would need to save a file listing the hbonds at each step, and then do some of your own postprocessing or analyses on these output files to determine how many times each hbond is found.  Currently there is no built-in function to do that part.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 13, 2010, at 7:02 AM, George Tzotzos wrote:

> Hi everybody,
> I wonder is there's a way that Chimera produces hbond occupancy statistics from amber trajectory files. 
> I can produce hbond information between a ligand and a receptor molecule frame by frame. As the ligand forms hbonds with different amino acid residues in the binding site during the trajectory, I'd like to work out which ones are the most frequently formed.
> Thanks in advance for your advice
> Best regards
> George

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