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

From: Eiros Zamora, Juan <>
Date: Sun, 10 Jan 2016 11:56:58 +0000

I use cpptraj inside bash scripts as such:

cpptraj <<- EOF
parm topology.prmtop
# Any commands you would normally use

Hopefully that works for you as well,


On 10 Jan 2016, at 05:12, 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
[Imperial College London] <>
Juan Eiros Zamora / PhD Student<> / +44 (0) 7783018326
Imperial College London
Imperial College Road SW7 2AZ | UK
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Received on Sun Jan 10 2016 - 04:00:03 PST
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