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Error to import simtk module from 13 tutorial

See original GitHub issue

Hi everyone, I try to replicate the code of tutorial 13 in my machine. But when I run the cell: from simtk.openmm.app import PDBFile from pdbfixer import PDBFixer from deepchem.utils.vina_utils import prepare_inputs

I get the error ModuleNotFoundError: No module named 'simtk.openmm' I already installed OpenMM.

Issue Analytics

State:
Created 2 years ago
Comments:13 (7 by maintainers)

Top GitHub Comments

1reaction

peastmancommented, Feb 4, 2022

Try changing it to just

from openmm.app import PDBFile

OpenMM 7.6 dropped the simtk at the start of the package name. However, it still includes stubs for the old packages, so they ought to work. Here’s what I get:

>>> from simtk.openmm.app import PDBFile
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
>>>

I don’t know any reason it wouldn’t work for you.

0reactions

peastmancommented, Feb 4, 2022

Very strange! I don’t understand why it isn’t accepting the old name.

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