Re: [AMBER] How to extract frames with particular hydrogen bonds only

From: Daniel Roe <>
Date: Thu, 3 May 2018 10:42:05 -0400


You can do this in cpptraj via a combination of 'hbond' and 'outtraj'.
First, generate hydrogen bond time series data with the hbond command:

parm myparm.parm7
hbond <hbond args> series uuseries UU.dat

See the manual for the description of the arguments available for
'hbond'. The time series data for each hydrogen bond contains a 1 for
the frame if the hydrogen bond is present and 0 otherwise. Once you've
got the hbond time series data, you can read it back in and in and use
'outtraj' with 'maxmin' to extract frames where the particular
hydrogen bonds are present, e.g.

parm myparm.parm7
readdata UU.dat index 1 name UU
outtraj maxmin UU:2 min 0.5 max 1.5
outtraj maxmin UU:3 min 0.5 max 1.5

Hope this helps,


On Wed, May 2, 2018 at 11:31 AM, Stejskal, Lenka
<> wrote:
> Hello Amber users!
> I want to ask whether anyone knows of a way to extract frames from a trajectory with a particular hbonds between particular residues. I have four hbonds and I would like to find out the percentage of the frames that have all of them, three of them….
> Thank you very much for your help!
> Lenka
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Thu May 03 2018 - 08:00:05 PDT
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