I use cpptraj inside bash scripts as such:
cpptraj <<- EOF
parm topology.prmtop
trajin trajectories.nc
# Any commands you would normally use
run
EOF
Hopefully that works for you as well,
Juan
On 10 Jan 2016, at 05:12, Robert Molt <rwmolt07.gmail.com<mailto:rwmolt07.gmail.com>> 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.
r.molt.chemical.physics.gmail.com<mailto:r.molt.chemical.physics.gmail.com>
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Juan Eiros Zamora / PhD Student
je714.ic.ac.uk<mailto:je714.ic.ac.uk> / +44 (0) 7783018326
Imperial College London
Imperial College Road SW7 2AZ | UK
http://www.icb-cdt.co.uk/
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Received on Sun Jan 10 2016 - 04:00:03 PST
