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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).


Settings

Biobb modules used

  • biobb_io: Tools to fetch biomolecular data from public databases.
  • biobb_model: Tools to model macromolecular structures.
  • biobb_chemistry: Tools to manipulate chemical data.
  • biobb_md: Tools to setup and run Molecular Dynamics simulations.
  • biobb_analysis: Tools to analyse Molecular Dynamics trajectories.
  • biobb_structure_utils: Tools to modify or extract information from a PDB structure file.

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 https://github.com/bioexcel/biobb_wf_protein-complex_md_setup.git
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 --py --user widgetsnbextension
jupyter-nbextension enable --py --user nglview
jupyter-notebook biobb_wf_protein-complex_md_setup/notebooks/biobb_Protein-Complex_MDsetup_tutorial.ipynb

Tutorial

Click here to view tutorial in Read the Docs


Version

2021.2