Re: [AMBER] identiy the step of interaction from an entire trajectory

From: Daniel Roe <>
Date: Mon, 2 Oct 2017 08:55:48 -0400


On Thu, Sep 28, 2017 at 3:10 PM, Thakur, Abhishek <> wrote:
> I want to know is there any way to identify that at which step this interaction has occurred?

Yes, but it's not straightforward. You essentially need to "grep" that
specific combination from the hydrogen bond vs time file (i.e. the
file written by the 'hbond' 'out' keyword). E.g.,

grep "(961+1637+)" solventhb.dat

Bridging time series data sets are on my infamous to-do list...

Hope this helps,


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 Mon Oct 02 2017 - 06:00:10 PDT
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