AMBER Archive (2009)

Subject: [AMBER] ptraj and prmtop

From: Beale, John (
Date: Wed Oct 14 2009 - 07:46:11 CDT

I am doing an MD run on a protein. For the first 1,000,000 or so steps I
was able to use ptraj to compute the rms and radius of gyration. Now,
for some reason, ptraj won't work for rms or radgyr (I am using the same
input filenames). If I look at the *.out file, there is an error
notation that says "PRMTOP does not contain %FLAG RADIUS_SET" and one
that says "WARNING in ptraj(): No input trajectories specified (trajin),


The trajin file is definitely in the script.


Everything is the same as it was when this was working. Is there a way
to edit the PRMTOP file to fix the %FLAG RADIUS_SET problem? Why isn't
ptraj recognizing the trajin file?








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