Re: [AMBER] Scripting CPPTRAJ Analysis Commands within a PBS Script

From: Kenneth Huang <>
Date: Sun, 10 Jan 2016 12:00:54 -0500

In my experience, it's as simple as-


cd A/
$AMBERHOME/bin/cpptraj -i analysis.ptraj

Where the relevant commands you'd want to run are all located in



On Sun, Jan 10, 2016 at 12:12 AM, Robert Molt <> wrote:

> Good evening,
> I wish to write a PBS script to analyze many trajectories using cpptraj.
> However, I do not know how to load a list of commands into cpptraj after
> opening cpptraj from a submission script (as one normally types the
> analysis commands after it begins execution).
> I apologize if this is more a computer science question to which I ought
> know the answer than Amber. I have not been successful in searching the
> Amber forums for an answer using a string of "cpptraj PBS" and the like
> --
> Dr. Robert Molt Jr.
> _______________________________________________
> AMBER mailing list

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Received on Sun Jan 10 2016 - 09:30:03 PST
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