Error when running ML-ddG-Blaabjerg-et-al colab notebook #11
Description
notebook link: https://colab.research.google.com/github/KULL-Centre/papers/blob/main/2022/ML-ddG-Blaabjerg-et-al/RaSPLab.ipynb
Error message:
During handling of the above exception, another exception occurred:
ModuleNotFoundError Traceback (most recent call last)
[<ipython-input-2-26b8f94c780a>](https://localhost:8080/#) in <module>
19 import datetime
20 import matplotlib
---> 21 from pdbfixer import PDBFixer
22 from simtk.openmm.app import PDBFile
23 from Bio.PDB.Polypeptide import index_to_one, one_to_index
[/usr/local/lib/python3.7/site-packages/pdbfixer/__init__.py](https://localhost:8080/#) in <module>
1 from __future__ import absolute_import
----> 2 from .pdbfixer import PDBFixer
3
[/usr/local/lib/python3.7/site-packages/pdbfixer/pdbfixer.py](https://localhost:8080/#) in <module>
33 __version__ = "1.5"
34
---> 35 import simtk.openmm as mm
36 import simtk.openmm.app as app
37 import simtk.unit as unit
[/usr/local/lib/python3.7/site-packages/simtk/openmm/__init__.py](https://localhost:8080/#) in <module>
17 'lib': version.openmm_library_path, 'path': _path}
18
---> 19 from simtk.openmm.openmm import *
20 from simtk.openmm.vec3 import Vec3
21 from simtk.openmm.mtsintegrator import MTSIntegrator
[/usr/local/lib/python3.7/site-packages/simtk/openmm/openmm.py](https://localhost:8080/#) in <module>
26 fp.close()
27 return _mod
---> 28 _openmm = swig_import_helper()
29 del swig_import_helper
30 else:
[/usr/local/lib/python3.7/site-packages/simtk/openmm/openmm.py](https://localhost:8080/#) in swig_import_helper()
18 fp, pathname, description = imp.find_module('_openmm', [dirname(__file__)])
19 except ImportError:
---> 20 import _openmm
21 return _openmm
22 if fp is not None:
ModuleNotFoundError: No module named '_openmm'
---------------------------------------------------------------------------
NOTE: If your import is failing due to a missing package, you can
manually install dependencies using either !pip or !apt.
To view examples of installing some common dependencies, click the
"Open Examples" button below.
---------------------------------------------------------------------------