[Chimera-users] H Bonds in MD simulation

Elaine Meng meng at cgl.ucsf.edu
Fri Jan 29 11:08:28 PST 2010

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.

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.

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 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 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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