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

From: Jason Swails <>
Date: Thu, 24 Oct 2013 11:42:54 -0400

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?


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Oct 24 2013 - 09:00:02 PDT
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