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 - 13:30:02 PDT
