Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb)

Based on the official GROMACS tutorial.

This tutorial aims to illustrate the process of setting up a simulation system containing a protein in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the T4 lysozyme L99A/M102Q protein (PDB code 3HTB), in complex with the 2-propylphenol small molecule (3-letter Code JZ4).


Biobb modules used

Auxiliar libraries used

  • nb_conda_kernels: Enables a Jupyter Notebook or JupyterLab application in one conda environment to access kernels for Python, R, and other languages found in other environments.
  • nglview: Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
  • ipywidgets: Interactive HTML widgets for Jupyter notebooks and the IPython kernel.
  • os: Python miscellaneous operating system interfaces
  • plotly: Python interactive graphing library integrated in Jupyter notebooks.
  • simpletraj: Lightweight coordinate-only trajectory reader based on code from GROMACS, MDAnalysis and VMD.

Conda Installation and Launch

git clone
cd biobb_wf_protein-complex_md_setup
conda env create -f conda_env/environment.yml
conda activate biobb_Protein-Complex_MDsetup_tutorial
jupyter nbextension enable python-markdown/main
jupyter-notebook biobb_wf_protein-complex_md_setup/notebooks/biobb_Protein-Complex_MDsetup_tutorial.ipynb

Please execute the following commands before launching the Jupyter Notebook if you experience some

jupyter-nbextension enable --py --user widgetsnbextension
jupyter-nbextension enable --py --user nglview


Click here to view tutorial in Read the Docs