Re: [AMBER] Error in hbond lifetime analysis

From: Daniel Roe <>
Date: Thu, 10 Aug 2017 15:29:17 -0400


On Tue, Aug 8, 2017 at 4:17 PM, Baig abdullah Al muhit
<> wrote:
> Hello everyone,
> (1). The number of hbond/molecule is 1.27 whereas it should have been near 3.5.

What are you basing the number of 3.5 on?

> (2). I couldn't calculate the lifetime of hbond by runanalysis command. Here's what I did.
> parm waterfinal.mol2 # My topology file
> trajin hbond.dcd # My trajcetory file (100 frames)
> hbond HB distance 3.5 angle 150 out hbvtime.dat avgout avhhb.dat # This gave me two files
> runrunanalysis lifetime HB out lifehb.dat

> ACTION OUTPUT: 34884 solute-solute hydrogen bond
> Does it mean I have a total of 34884 bonds over 100 frames?

This is the total number of unique hydrogen bonds found in all
trajectory frames. They will be found in 'avhhb.dat' according to your

> Error says:Warning: 'HB' selects no data sets.
> Error: No data sets selected.
> Error: lifetime: Could not add data sets.
> So, I can calculate the number of hbonds but not the lifetime.Can anyone point out the mistake in my approach?

There are three problems with your input. One is that you haven't
specified the 'series' keyword for the 'hbond' command, so cpptraj
isn't saving the time series data. The second is that you need to
specify a data set aspect as well as data set name to access the hbond
lifetime series data ([UU] for solute-solute and [UV] for
solute-solvent). The third is that until you actually perform a
trajectory processing run, the hbond time series data does not exist.
Cpptraj prints a warning stating this:

Warning: Some Actions currently in Action list need to be run in order to create
Warning: data sets. Try processing currently loaded trajectories with 'run' or
Warning: 'go' to generate these data sets.

So you need a 'run' in between your 'hbond' command and 'runanalysis'
command. There is an example of performing 'lifetime' analysis
specifically on 'hbond' data given in the Amber manual (section
28.10.7 lifetime, page 665) that you may find useful.

Hope this helps,


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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 Aug 10 2017 - 12:30:03 PDT
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