Re: [AMBER] Amber Tools cpptraj woes

From: Jason Swails <>
Date: Mon, 9 Sep 2013 17:17:44 -0400

On Mon, Sep 9, 2013 at 3:59 PM, Geoffrey Gray <> wrote:

> Yes, it does, thank you very much, I really appreciate your response!

In case it helps, I'll explain why deleting 'quit' fixes cpptraj.

Cpptraj and ptraj both operate by building a queue of 'actions' and
'analyses' based on the commands you give it. After you're 'done'
specifying what you want to do to each frame either by typing 'go' or
hitting the end of file (Ctrl-D in interactive mode, or just the end of the
file in a script), (cp)ptraj reads each frame in each input trajectory one
at a time, passing it to each action in the queue in the same order you
made the commands. [1] This stage generates a bunch of data sets,
depending on the actions that you specified.

After this stage, the data sets that were generated are passed to the
analysis queue where they are processed and printed to files.

Cpptraj has a number of commands that ptraj does not. One of those
commands is 'quit', which tells cpptraj to exit immediately (i.e., before
any actions or analyses have been performed). Since ptraj does not
recognize that command, it simply prints out an informative message and
moves on. In my experience, quit is predominantly used in interactive mode
(rarely in scripts), for this very reason.


[1] A notable exception is 'trajout' which always executes at the end and
'trajin's, which always execute at the beginning. The 'outtraj' action (in
cpptraj) is the same as a trajout, except it writes a trajectory at its
location in the action queue.

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 09 2013 - 14:30:03 PDT
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