Re: [AMBER] CPPtraj not producing outputs

From: Jason Swails <>
Date: Wed, 18 Sep 2013 12:09:02 -0400

On Wed, Sep 18, 2013 at 11:51 AM, Neha Sikka <> wrote:

> Hi all,
> I'm new to Amber and have been trying to use CPPtraj to write some simple
> RMSDs and cluster. However, CPPtraj will not write any output files for me.
> Previously, when I force quit the process without first quitting CPPtraj,
> my output file would be written.
> For example,
> after loading in my trajectories and assigning a reference, I would use the
> command "rms :1-140 reference mass out <filename>"
> Does anyone know what could be wrong or a possible solution?

cpptraj does not do anything until explicitly told to do so. You can tell
cpptraj to 'run' by using either the 'go' command or by sending the EOF
character (Ctrl-D for an interactive session, or the end of the script file
for a scripted session). If you tell it to 'quit', it will do so... without
running anything. My guess is you are quitting before cpptraj has a chance
to execute any commands. (The 'quit' command should rarely, if ever,
appear in a script -- it is typically useful only in interactive mode)

However, as a general rule of thumb, you should always tell us _exactly_
what you did (i.e., send commands and input scripts), as well as _exactly_
what happened (send program output), and what you expected/wanted to
happen. Telling us what you tried to do or trying to describe what you did
leaves us guessing at what the source of the error really is. (a mis-typed
command? a mis-used command? an actual bug? some unexpected, but normal,
behavior? etc.).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Sep 18 2013 - 09:30:03 PDT
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