Re: [AMBER] trajout frames that statisfy hbond criteria

From: Daniel Roe <>
Date: Tue, 23 Sep 2014 08:01:25 -0600


This can be done using the 'outtraj' command with the 'maxmin'
keyword. It can be done in 2 stages. In the first stage you generate
hydrogen bond data vs time using the 'hbond' command with the 'series'
keyword, e.g.:

hbond H1 series .N,H,C,O

This will create a data set for each solute-solute hbond detected,
named H1[solutehb]:X, where X is a unique internal index for that
hydrogen bond. The name of each of these data sets is listed after the
run completes, 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

These time series data sets contain a '1' when the hydrogen bond in
question is present and '0' when not. After running (because the data
sets are not actually created until hydrogen bonds are detected) you
can write these out to a separate data set for further processing or
use them in the same run (or both). Once you have the data it can be
used with 'outtraj' with the 'min' and 'max' keywords set so that data
with '1' indicates frames should be written. So the entire command
sequence might look like:

hbond H1 series .N,H,C,O
# Save time series data for later just in case
writedata solutehb.dat H1[solutehb]
# Write out frames where "GLU_13.O-VAL_2.N-H" is formed
outtraj netcdf maxmin H1[solutehb]:24 min 0.5 max 1.5

A related command is 'filter', which lets you process only frames that
match certain criteria with subsequent actions.

Hope this helps,


On Tue, Sep 23, 2014 at 5:57 AM, George Green <> wrote:
> I have been doing some hydrogen bond analysis and have obtained occupancies
> and other data for solute-solute hydrogen bonds using AMBER 13.
> I would like to output some frames from the trajectory based on this
> analysis, so that I can look at structures that have certain specific
> hydrogen bonds. e.g. If there is a hbond between res37 and res44, I would
> like to output all frames that possess this interaction.
> Is there any way to do this with cpptraj?
> many thanks for your assistance.
> _______________________________________________
> 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 Tue Sep 23 2014 - 07:30:02 PDT
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