Re: [AMBER] ptraj hbond output format

From: Daniel Roe <>
Date: Fri, 6 Dec 2013 17:05:38 -0700


Cpptraj will write out total # of solute-solute hbonds (and optionally
solute-solvent hbonds and # bridging waters) to the file specified by 'out
<filename>'. If you want raw time series data, you can specify 'series',
which will lead to a data set being created for each hbond seen over the
course of the input trajectory; solute-solute hbonds have aspect [solutehb]
and solute-solvent hbonds have aspect [solventhb]. These data sets have 1
for hbond present and 0 otherwise. You can write them all to a file once
trajectory processing is done via the write command, for example:

parm input.parm7
hbond HB out hbond.dat .N,C,H,O series avgout hbavg.dat printatomnum
write solutehb.dat HB[solutehb]

This runs the Hbond command looking for hydrogen bonds in the given mask
selection (in this case just some protein backbone atoms). This will
generate 3 files: hbond.dat will have the total # solute-solute hbonds,
hbavg.dat will have the average occupancies etc for each hbond seen, and
solutehb.dat will have the raw occupancy vs time for each hbond (in
columns). The 'printatomnum' command will print the atom number for each
hbond in hbavg.dat. You can obtain grace or gnuplot style output for
hbond.dat/solutehb.dat by changing the extension to .agr/.gnu respectively.

Hope this helps,


PS - You can also run lifetime analysis on the data generated by adding
something like this after the 'run' command:

runanalysis lifetime HB[solutehb] out lifehb.dat

On Fri, Dec 6, 2013 at 6:39 AM, Andre C. Stiel <
> wrote:

> hi all,
> is there a way to change the output format of the hbond command in
> ptraj....
> I mean the graphical .**x*.. style is quite nice, but for something
> sheer occupancy number to plot against the simulation time would be nicer.
> Is there a way to accomplish that?
> Cheers
> André
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Dec 06 2013 - 16:30:02 PST
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