Re: [AMBER] bug when using the "parmout" command ?

From: Jason Swails <>
Date: Thu, 24 Oct 2013 13:09:27 -0400

On Thu, Oct 24, 2013 at 12:31 PM, Vlad Cojocaru <> wrote:

> I tested it and "outparm" produces exactly the same error.

This must be due to the fact that ArgumentList is actually being pulled
from somewhere else. You can look at the source code, has_key() is
definitely a defined attribute of ArgumentList, and all of the ParmEd tests
must fail when parmout and outparm do not work. It is impossible for this
error to occur when the correct ArgumentList is being imported into ParmEd,
so either there is an old ParmedTools package somewhere that is in
PYTHONPATH or ParmedTools somehow got corrupted in your $AMBERHOME/bin
directory. What does the command:

grep has_key $AMBERHOME/bin/ParmedTools/

return? Does it appear to be present?

You can try to re-install ParmEd and see if that fixes things.

cd $AMBERHOME/AmberTools/src/parmed
make uninstall
make install

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Oct 24 2013 - 10:30:02 PDT
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