Re: [AMBER] problems with the keyword "append" in trajout command...

From: Jason Swails <>
Date: Sat, 13 Oct 2012 20:39:43 +0200

On Fri, Oct 12, 2012 at 8:46 PM, Shashidhar Rao <>wrote:

> I am attempting to append AMBER trajectory data to an existing trajectory
> file in the netcdf format (with the .nc extension) using the following
> command:
> trajout append nobox
> where was previously created using the command "trajout
> nobox"
> however, I notice that the process of appending the file has not been
> done. The file size of the new file is almost the same as the older one,
> instead of doubling. I found the same issue when I used the default ascii
> file format for the output. The manual says that the append option works
> only with AMBER trajectory format and netcdf format (page 173 of AmberTools
> manual).
> Any insights into this issue would be helpful. Currently, I am using the
> bypass solution of generating individual trajectory files with different
> names.

As a workaround, why not just create the entire trajectory at once? You
can use many trajin commands in a single ptraj script. So something like

trajin traj1.mdcrd
trajin traj2.mdcrd
trajin traj3.mdcrd
trajin traj4.mdcrd

[do your operations here, like strip or RMS, or image, etc.]

trajout total.mdcrd

This will create "total.mdcrd" that has every frame in the 4 trajectories
loaded in ptraj (or cpptraj).


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Sat Oct 13 2012 - 12:00:03 PDT
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