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

From: Vlad Cojocaru <>
Date: Thu, 24 Oct 2013 18:31:41 +0200

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


On 10/24/2013 05:42 PM, Jason Swails wrote:
> On Thu, Oct 24, 2013 at 11:06 AM, Brian Radak <> wrote:
>> Hi Vlad,
>> Disclaimer: I'm a parmed user, not a developer.
>> Isn't the command "outparm" not "parmout"? Or is that synonymous syntax?
> I'd call it a mistake. parmout and outparm are two different commands, and
> I see little reason to use parmout in general. The idea was to mirror what
> ptraj (and cpptraj) do. Namely, the "parmout" statement is analogous to
> "trajout" and will print out a single prmtop file at the very end of the
> script (after 'go' or EOF). "outparm", on the other hand, is analogous
> to "outtraj" in cpptraj and allows you to print out prmtop files wherever
> you want in the action stack.
> The error Vlad was getting is weird, though. The code for parmout and
> outparm is identical (and has_key is a defined method of ArgumentList).
> This error doesn't make much sense to me (especially when 'outparm'
> appears to work?). In the simple script Vlad gave, parmout and outparm
> should work identically. Perhaps something in your original shell was
> corrupted when you tried it the first time? If the 'outparm' command
> works, can you change back to 'parmout' and check it?
> Thanks,
> 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 - 10:00:03 PDT
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