Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file?

From: Daniel Roe <>
Date: Mon, 28 Aug 2017 08:39:36 -0400


What you want to do is currently not entirely possible with cpptraj.
Getting the coordinate/velocity/force data could potentially be done
but it's not straightforward.

I assume the trajectory is in NetCDF format. FYI NetCDF distributions
come with a tool called 'ncdump' which can be used to extract values
from NetCDF files in text format. For example:

ncdump -v coordinates <file>

can be used to extract the coordinates from an Amber NetCDF trajectory
file. 'ncdump -h <file>' can be used to see which variable names are
present in the file.

If you would like this functionality to be a part of cpptraj feel free
to add a feature request to the cpptraj GitHub page:


On Sun, Aug 27, 2017 at 5:41 PM, Jewgeni Starikow
<> wrote:
> Dear all,
> I have generated an AMBER trajectory with coordinates, velocities and
> forces at every time point. It is readily readable with the standard
> CPPTRAJ routine.
> Now, from this point on, how could I write out the relevant data sets
> in some (text or binary) file readable in some straightforward way?
> I would greatly appreciate ordering my corresponding output file like
> as follows:
> Atom-Nr Time CoordX CoordY CoordZ VelocX VelocY VelocZ
> ForceX ForceY ForceZ
> ... ... ... ... ... ... ... ...
> ... ... ...
> ...etc., etc., etc. ...
> Which set of the CPPTRAJ commands would be most appropriate for the
> above-outlined case?
> Respectfully yours,
> Evgeni B. Starikov
> _______________________________________________
> AMBER mailing list

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 Aug 28 2017 - 06:00:06 PDT
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