Question:
I am working in the MD simulation on GROMACS 2023 with Protein+Lipid (as ligand) complex. I have encountered an error, and I already tried all available option to perform MD run with Python version 3.7 and both versions of the networkX module (networkX 1.11, and 2.3). I have also tried to downgrade the python version 2.7 with networkX 1.11, but system got crashed probably because python integrated with Ubuntu OS 23.04. Can anyone help me to sort out this error, because I have already tried so many times.
Error:
enff_charmm2gmx_py2.py", line 51, in
port networkx as nx
portError: No module named networkx
The error message portError: No module named networkx indicates that the Python environment you are using does not have the networkx module installed. This module is required by the cgenff_charmm2gmx_py2.py script, which suggests that it is a Python 2 script given the “py2” in the name.
My suggestion:
Python 2 reached the end of its life on January 1, 2020, which means it no longer receives updates, including security updates. Unless you have a compulsion related to the platform, please switch to python3. Use conda to create a separate environment for cgenff.
Create a new conda environment with python 3.7 or 3.5.2, and install networkx version 2.3 within the environment (conda install networkx=2.3 numpy)