Hi Jason,
Thanks so much for prompt reply. ... just to note that, in the examples of
parmed in the Ambertools14 manual, it was put down like:
addLJType .57 0.0 0.0
a correction in the next update.
Thanks again.
Ying-chieh
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Tuesday, November 4, 2014 1:09 AM
To: amber.ambermd.org
Subject: Re: [AMBER] error message of addLJType of parmed: Action addLJType
failed. UnhandledArgumentWarning: 0.0 0.0
On Tue, 2014-11-04 at 00:11 +0800, sun wrote:
> Hi,
> below are my output error message and input information. ... Any idea?
> thanks.
>
> Ying-chieh
> -------
> command line:
>
> parmed.py -p p82-82Awatbox2-a.prmtop -i s4_5-parmed-vdw-c.in
>
> input file:
> ::::::::::::::
> s4_5-parmed-vdw-c.in
> ::::::::::::::
> setOverwrite True
> addLJType .89 0.0 0.0
> outparm p82-82Awatbox2-b.prmtop
> quit
>
> output with error message:
> Loaded Amber topology file p82-82Awatbox2-a.prmtop
> ['s4_5-parmed-vdw-c.in'] Reading actions from s4_5-parmed-vdw-c.in
>
> Files are overwritable
> Action addLJType failed
> UnhandledArgumentWarning: 0.0 0.0
Unhandled arguments indicates that you are using the command incorrectly.
Use the "help" function in ParmEd to get the command
syntax:
swails.batman ~ $ parmed.py -n
Reading input from STDIN...
> help addLJType
addLJType <mask> [radius <new_radius>] [epsilon <new_epsilon>]
[radius_14 <new_radius14>] [epsilon_14 <new_epsilon14>] [parm
<idx>|<name>]
Turns given mask into a new LJ atom type. It uses the radius and Rmin
from
the first atom type in <mask> if new_radius or new_epsilon aren't
provided
The syntax for this command has changed slightly since the original release
of ParmEd. The radius and epsilon parameters are now keyword-input. So you
would need to change your command to:
addLJType .89 radius 0.0 epsilon 0.0
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 03 2014 - 19:00:02 PST
