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: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html 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): http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ ensembles2.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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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