Re: [AMBER] Amber Tools cpptraj woes

From: Geoffrey Gray <>
Date: Mon, 9 Sep 2013 23:32:21 -0400

Thank you very much for your help. I appreciate your response and
explanation a great deal.


On Mon, Sep 9, 2013 at 5:17 PM, Jason Swails <> wrote:

> 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.
> HTH,
> Jason
> [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
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Sep 09 2013 - 21:00:04 PDT
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