[Chimera-users] H Bonds in MD simulation

snoze pa snoze.pa at gmail.com
Fri Jan 29 11:59:11 PST 2010

Thank you very much Elaine. It is working fine now. I was using wrong command

from chimera import runCommand
for HbonDNum in range(1, 1000):
        runCommand("hbonds  saveFile ligand.%03d.hbonds" %  HbonDNum)

On Fri, Jan 29, 2010 at 1:08 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi S,
> If you wanted only how many H-bonds there are at each step sent to a file,
> you can just save the contents of the Reply Log (under Favorites menu).  You
> would define the script in MD Movie, then clear the Reply Log, then run the
> trajectory through from start to end one time (with Loop turned off).  Then
> click Save on the Reply Log to save its contents to a text file.
> If you wanted the detailed results of which atoms are H-bonding and their
> distances at each step, it can be done with the "saveFile" option of the
> "findhbond" command.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findhbond.html>
> The MD Movie per-frame script capability allows inserting the frame number
> in the filename so you can get a different H-bond results file for each
> step.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>
> For example, the per-frame script could have something like
> findhbond saveFile ~/Desktop/hbondinfo-<FRAME>.txt
> (plus any other options of that command you might want) which puts all the
> information from frame 1 into hbondinfo-001.txt, frame 2 hbondinfo-002.txt,
> ... files on my mac Desktop.
> Elaine
> -----
> 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
>                     http://www.cgl.ucsf.edu/home/meng/index.html
> On Jan 29, 2010, at 10:02 AM, snoze pa wrote:
>> I checked the results with molmol and it seems chimera results are
>> correct. I want to save the number of hbonds in each frame. When I use
>> the command hbond in chimera script movie menu command then it prints
>> correct number of hbonds in every frame. Can you help me how to save
>> the results from each frame(total no of hbonds).
>> thank you
>> S
>> On Thu, Jan 28, 2010 at 4:59 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> I forgot to mention: from looking at the images, I would say the Chimera
>>> results are more reasonable, because that's how beta-sheets form, with
>>> strand-strand hydrogen bonds.  In the VMD view, some strands lack H-bonds
>>> to
>>> the next strand in the sheet, or only have one.
>>> Of course, these statements are only qualitative, but it was my first
>>> impression.
>>> Elaine
>>> On Jan 28, 2010, at 2:36 PM, snoze pa wrote:
>>>> Hi Elaine, Thanks for your help. But somehow I am getting different
>>>> number of bonds in vmd and chimera. A snap shot of the  figure is
>>>> shown below.
>>>> http://img191.imageshack.us/img191/9084/screenshotva.png
>>>> In VMD the Hbonds are calculated by show Hbonds and protein. Vms shows
>>>> 24 hbonds while chimera shows 38 hbonds. I don't know how to justify
>>>> this. I will highly appreciate your help. A snapshot is shown in the
>>>> link
>>>> http://img191.imageshack.us/img191/9084/screenshotva.png
>>>> Thanks
>>>> s
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