[Chimera-users] hbond analysis

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 9 09:32:00 PDT 2010

Hi George,
There is a FindHBond tool (in menu under Tools... Structure Analysis) and equivalent command "findhbond" that can be used on trajectory frames the same way as on single structures. The findhbond tool and command have the same capabilities, and many options.  Either way, using a recent version of Chimera (version 1.5, so a daily build) you could find H-bonds between two specified sets of atoms, but the command allows scripting.


To view trajectories, start the "MD Movie" tool (in menu under Tools... MD/Ensemble Analysis), and specify the type of input and names/locations of input files, in this case your Amber trajectory and prmtop.  Here is more information about MD Movie:


I would just show one frame of that trajectory (rather than playing continuously) and then try using the "findhbond" command to figure out what options you need.  Once you have figured that out, you can run the calculation at every trajectory frame by putting that command in a per-frame script in MD Movie.  There is an example here for calculating all H-bonds:

Your "findhbond" (or "hbonds") command would have some different arguments.  For example, to get only the ligand-receptor H-bonds you would probably want to select the ligand ahead of time and then use the "selRestrict" option with a receptor specification (it depends on your trajectory as to what that would be).  To save the results, you might want to use the "log" or "saveFile" option.

This previous post discusses saving H-bond information calculated from trajectories:

This tutorial includes viewing an Amber trajectory and using a per-frame script to find H-bonds:

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 Jun 9, 2010, at 9:02 AM, George Tzotzos wrote:

> Hi everybody,
> Is there a way in CHIMERA allowing to detect hbond between ligand and receptor from AMBER trajectory files?
> Best regards
> George

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