Re: [AMBER] ParmEd error

From: Jason Swails <>
Date: Mon, 8 Nov 2021 08:58:24 -0500

On Sat, Nov 6, 2021 at 6:34 AM Sangeetha B <> wrote:

> Dear Jason,
> That was my silly mistake.
> I found this string in the modified ff, which I ignored to check because I
> never got any warnings before.
> Correcting it solved my problem and I am able to convert the topology.
> Thanks a lot for pointing that out.
> But still the problem of "parmed doesn't load" still exists.
> When I try to load parmed by typing "parmed" in the terminal, I get the
> following error.
> Traceback (most recent call last):
> File "/mnt/c/amber20/bin/parmed", line 33, in <module>
> sys.exit(load_entry_point('ParmEd==0+unknown', 'console_scripts',
> 'parmed')())
> File "/mnt/c/amber20/bin/parmed", line 25, in importlib_load_entry_point
> return next(matches).load()
> StopIteration
> Any help regarding this?

There is clearly a problem with the installation of the ParmEd executables
(although the libraries are installed correctly). What are the contents of
$AMBERHOME/bin/parmed? In particular, the first line is important (called
the "shebang" or "shell-bang" line), since it specifies the
executable/shell that should be used to execute the rest of the script.

It *should* be `#!/mnt/c/amber20/miniconda3/bin/python` or something like
that (it should point to the miniconda installation inside the Amber
install directory itself). If it reads something else, then it's likely
trying to execute the script with a Python executable that doesn't know
where to look for ParmEd (and therefore can't find it).

If you installed AmberTools using CMake according to the directions in the
manual, ParmEd should have been installed correctly. That said, it's
difficult to tell why your parmed is trying to load with the wrong Python,
as there are a lot of different ways this could happen.


Jason M. Swails
AMBER mailing list
Received on Mon Nov 08 2021 - 06:00:03 PST
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