Hi David and others:
Thank you for helping me to debug that.
When I enter just
./pdb4amber -h"
it returns:
Traceback (most recent call last):
File "/home/andriy/amber22/bin/./pdb4amber", line 33, in <module>
sys.exit(load_entry_point('pdb4amber==22.0', 'console_scripts',
'pdb4amber')())
File "/home/andriy/amber22/bin/./pdb4amber", line 22, in
importlib_load_entry_point
for entry_point in distribution(dist_name).entry_points
File
"/home/andriy/amber22/miniconda/lib/python3.10/importlib/metadata/__init__.py",
line 969, in distribution
return Distribution.from_name(distribution_name)
File
"/home/andriy/amber22/miniconda/lib/python3.10/importlib/metadata/__init__.py",
line 548, in from_name
raise PackageNotFoundError(name)
importlib.metadata.PackageNotFoundError: No package metadata was found for
pdb4amber
Strange, isn't it?
I will try using just tleap.
Best regards,
Andriy
--------------------------------------------------
Dr. Andriy Kovalenko
Adjunct Professor
Department of Biological Sciences
University of Alberta
CW 405, Biological Sciences Bldg.
Edmonton, Alberta, Canada T6G 2E9
Tel: 780-940-7477 (cell)
e-mail: andriy.kovalenko.ualberta.ca
On Tue, Apr 11, 2023 at 2:22 PM David A Case <david.case.rutgers.edu> wrote:
> On Tue, Apr 11, 2023, Andriy Kovalenko via AMBER wrote:
> >
> >I have installed AmberTools from Amber22 (the latest version) on my Dell
> >Ubuntu Linux desktop.
> >
> >When running the *pdb4amber* part, I get an error message:
> >
> >~/amber22/bin$ ./pdb4amber -i alanine-dipeptide_noHydrogen.pdb -o
> >alanine-dipeptide__amber.pdb
> >Traceback (most recent call last):
> > File
>
> >"/home/andriy/amber22/miniconda/lib/python3.10/importlib/metadata/__init__.py",
> >line 548, in from_name
> > raise PackageNotFoundError(name)
> >importlib.metadata.PackageNotFoundError: No package metadata was found for
> >pdb4amber
>
> Hi Andriy (and others):
>
> Simple debugging questions:
>
> 1. Just to help in debugging, just try "pdb4amber -h": do you get the usage
> message?
>
> 2. Is your input file, alanine-dipeptide_noHydrogen.pdb, actually a
> plain-text PDB-format file? The metadata references may be coming from
> parmed (not sure), which might(?) have misidentified the format of the
> input
> file.
>
> Workaround is to just not use pdb4amber. :-) Your usage above is not
> correct: pdb4amber will not add hydrogens to a file that is missing them
> (unless you add the --reduce flag.) But tleap will do that for you, so you
> don't need (or want) pdb4amber for that part.
>
> ...hope this helps....dac
>
>
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Received on Tue Apr 11 2023 - 14:30:02 PDT
