[Chimera-users] H Bonds in MD simulation

snoze pa snoze.pa at gmail.com
Thu Jan 28 13:06:32 PST 2010

Thanks Elaine for your prompt reply. Do you think if it is good to
calculate the hbonds after every 10ps snapshot from hbonds menu. I
want to count how many hbond are lost with time. When I am using this
trick then I can see no more broken hbonds. Also another question
related to Relax constraints, it is 0.4 A; what that mean? is it same
as donor acceptor atom distance?
thank you.

On Thu, Jan 28, 2010 at 1:09 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>
> 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.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>
> 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.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>
> The Trajectories tutorial, part 1, also includes using a per-frame script to
> calculate H-bonds:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part1>
> I hope this helps,
> Elaine
> -----
> 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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