# Regarding the error of MD run with CHARMM36 force field

**URL:** <https://gromacs.bioexcel.eu/t/regarding-the-error-of-md-run-with-charmm36-force-field/7593>\
**Category:** User discussions\
**Tags:** forcefield, mdrun, installation-error, simulation-setup\
**Created:** [November 9, 2023, 11:28am UTC](https://gromacs.bioexcel.eu/t/regarding-the-error-of-md-run-with-charmm36-force-field/7593 "2023-11-09T11:28:28Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Praveen](https://avatars.discourse-cdn.com/v4/letter/p/3ec8ea/32.png) [@Praveen](https://gromacs.bioexcel.eu/u/Praveen)\
**Post date:** [November 9, 2023, 11:28am UTC](https://gromacs.bioexcel.eu/t/regarding-the-error-of-md-run-with-charmm36-force-field/7593/1 "2023-11-09T11:28:28Z")

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GROMACS version: 2023  
GROMACS modification: No

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

Thanks for your help.

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**Author:** ![deepakshilkar](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/deepakshilkar/32/2612_2.png) [@deepakshilkar](https://gromacs.bioexcel.eu/u/deepakshilkar)\
**Post date:** [November 10, 2023, 12:52am UTC](https://gromacs.bioexcel.eu/t/regarding-the-error-of-md-run-with-charmm36-force-field/7593/2 "2023-11-10T00:52:00Z")

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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`)

Use [cgenff\_charmm2gmx\_py3\_nx2.py](http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/cgenff_charmm2gmx_py3_nx2.py). It should now work within this environment.