Re: [AMBER] hbond lifetime

From: Daniel Roe <>
Date: Wed, 10 Sep 2014 14:27:08 -0600


On Wed, Sep 10, 2014 at 2:13 PM, George Tzotzos <> wrote:
> trajin
> hbond H1 series acceptormask :126&.N*,O* donormask :1-125&.N*,O*
> hbond out hb.dat dist 3.0 avgout avg.dat \
> bridgeout bridgeout.dat solventdonor :WAT solventacceptor :WAT&.O
> go
> runanalysis lifetime H1 [hb.dat] out life.dat

The data set aspects generated by 'hbond series' are [solutehb] for
solute-solute hydrogen bonds and [solventhb] for solvent-solute
hydrogen bonds (note that aspect information is listed for all actions
that use them in the cpptraj section of the Amber 14 manual). Since
you have named your data set H1 and you are looking for solute-solute
hydrogen bonds, you should refer to the data set as 'H1[solutehb]'. If
you're ever unsure as to how data sets are named you can refer to your
cpptraj output after a run. You should see a summary of data set names
etc in the DATASETS: part of the output, e.g.:

  20 data sets:
        H1[UU] "H1[UU]" (integer), size is 100
        H1[solutehb]:24 "GLU_13.O-VAL_2.N-H" (integer), size is 100
        H1[solutehb]:104 "TYR_11.O-ILE_4.N-H" (integer), size is 100

So in summary the analysis command you want should look like:

runanalysis lifetime H1[solutehb] out life.dat

Hope this helps,


> The script produces: avg.dat; bridgeout.dat and hb.dat. If fails to produce life.dat due to Error: lifetime: No datasets selected.
> Any help in improving the script will be much appreciated.
> Regards
> George
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Wed Sep 10 2014 - 13:30:04 PDT
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