[Chimera-users] question on monitoring hydrogen bonds

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 3 16:11:19 PST 2006

Hi Stacy,
Can do!
You can define a script to execute at each frame played (see the  
Per-Frame menu in MD Movie).  This script can run the H-bond  
calculation.  Each time it is run, the number of H-bonds detected is  
reported in the Reply Log, and further, you can save all the H-bonding  
information to a file (atom names, distance, etc.).  I think it would  
have to be a different file for each step. The Reply Log contents (with  
the counts) can be saved in one file after you've played through the  
whole trajectory, however.

You may have used the graphical interface of FindHBond already; the  
command "hbonds" can do all of the same things.  You would designate  
the per-frame script as "Chimera commands" and in the script area,  
enter "hbonds" along with any appropriate arguments.

Here is the man page for the hbonds command:

Arguments to the command include:
selrestrict  - allows the calculation to be limited to H-bonds with at  
least one end atom (donor or acceptor) selected, or exactly one end  
atom selected, or both end atoms selected

distSlop, angleSlop - allows criteria to be relaxed more or less than  
the default amount

saveFile - allows specification of an output filename

Our newest tutorial includes an example of using the hbonds command  
(aka "findhbond") in an MD movie script (near the end of part 1):

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 3, 2006, at 12:50 PM, knutsost wrote:

> Hi:
> I am interested in monitoring the hydrogen bonds which form/break
> between specific residues over the course of a MD simulation in CHARMM.
>   I am wondering if you have any way to record things like bond counts
> over time for the set of residues, or just to spit out a list of the
> bonds which form and break over the trajectory time course?  I really
> appreciate any help you could give me with this!  Thanks,
> Stacy Knutson
> Research Associate
> Wake Forest University
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