[Chimera-users] Hbond analysis in trajectories

Marek Maly marek.maly at ujep.cz
Tue Dec 20 18:13:58 PST 2011

Hi George,

if you would like to do hbond analyses of Amber trajectory, you may do it  
within the framework of Amber software. There are now (in Amber11) two  
different possibilities using (i) ptraj or (ii) cpptraj in combination  
with action
command "hbond". Check AmberTools manual.

In case you would like to analyze H-bonds between ligand and receptor only,
I would use ptraj version twice.

With defined donors only from ligand and acceptors only from receptor in  
the input file.

The opposite case (donors only from R and acceptors only from L)

     Best wishes,


Dne Tue, 20 Dec 2011 23:35:34 +0100 Elaine Meng <meng at cgl.ucsf.edu>  

> Hi George,
> You would need to define a per-frame script in MD Movie that includes  
> the findhbond command.  First just use the regular command line and the  
> manual page to figure out what command options you need.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>
>> From what you said it would probably include "selRestrict any" and "log  
>> true" (send to Reply Log instead of file... then at the end you can  
>> save the Reply Log contents to a file).
> Once you know the proper command, then enter it as a per-frame script in  
> MD Movie.  From the MD Movie menu, choose Per-Frame... Define script.  
> Enter the hbond command as a script to be interpreted as Chimera  
> commands.  Then you would probably want to clear the Reply Log (under  
> Favorites in the menu, has a "Clear" button on it), turn off looping in  
> MD Movie, and just play from start of trajectory to end to save all the  
> H-bond info into the log.  Then use the Save button on the Reply Log to  
> save to file.
> There is a similar per-frame script example in the  
> "Trajectories/Ensembles" tutorial, part 1:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part1>
> Besides saving everything to the log, another possibility is to make the  
> script write a separate output file for each step, if that is more  
> convenient for you.
> 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 Dec 20, 2011, at 11:29 AM, George Tzotzos wrote:
>> I'm trying to analyse Hbond formation during a 2ns AMBER trajectory  
>> involving receptor ligand complex. The trajectory loads as expected.  
>> I've selected the ligand and I checked the boxes "Only find H-bonds  
>> with at lease one end selected" and "Write information to file" .
>> The output hbond.info contains information of a single frame.
>> My question is whether there's a way by means of which information of  
>> ALL frames can be printed out.
>> Many thanks and best regards
>> George
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