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

From: Vlad Cojocaru <>
Date: Thu, 24 Oct 2013 19:15:31 +0200

These are the 2 lines output by "grep has_key
$AMBERHOME/bin/ParmedTools/ " ..

       if arg_list.has_key('netcdf'):
       if arg_list.has_key('netcdf'):

I will try reinstalling...


On 10/24/2013 07:09 PM, Jason Swails wrote:
> 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

Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]
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Received on Thu Oct 24 2013 - 10:30:03 PDT
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