Hello, I am currently performing analysis of MD runs from Amber using the
AmberTools 13 suite and am running into problems using the cpptraj program.
I have looked through the documentation and test scripts to no avail.
Strangely, when I use ptraj the scripts work. I had wanted to use some of
the features available solely to cpptraj (spec. Jcoupling). Here are some
examples
Script
###########################
# Analyzes atomic fluctuations
#
parm peptide3.prmtop
trajin temp-300_dev2.vmd.mdcrd
atomicfluct :TYR mass out tyr-flx.dat
quit
###########################
When I run
$AMBERHOME/bin/ptraj peptide3.prmtop -i fluct.in
the analysis works, but when I run
$AMBERHOME/bin/cpptraj peptide3.prmtop -i fluct.in
the output from the job is the same, but the data files specified in the
script (spec. try-flx.dat) is not writted. Thank you for your help and if
you need more information I am happy to provide it.
Geoffrey Gray
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Received on Mon Sep 09 2013 - 12:00:03 PDT
