[Chimera-users] H Bonds in MD simulation

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 28 11:09:56 PST 2010

Hi S,
The H-bonds do not automatically recalculate.  Instead of using  
findhbond one time before playing the trajectory, it should be used at  
each step.  This can be done with a per-frame script.  On the MD Movie  
player dialog, choose "Per-Frame... Define script" and specify that  
the script is in "Chimera commands."  Then enter whatever commands you  
want to execute at each step.  The MD Movie documentation includes an  
example with calculating H-bonds:

In your case it could be as simple as one "findhbond" command.  First,  
I recommend trying the command in the regular Command Line to figure  
out which keywords and options you want.

If there are protein ribbons shown, another command you might want to  
include in your per-frame script is "ksdssp" to recalculate secondary  
structure assignments.

The Trajectories tutorial, part 1, also includes using a per-frame  
script to calculate 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 Jan 28, 2010, at 10:51 AM, snoze pa wrote:

> Dear Chimera Users,
> I am analyzing a MD trajectory in chimera. After selecting H binds
> when I am playing the trajectory, then it always shows the hydrogen
> bond. Though some of the bonds are broken during the simulation but it
> always connect the step 1 h bonds connected.. How can I show the h
> bonds which breaks during the simulation.
> Thank you very much for your help.
> S

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