Protein MD Setup tutorial using BioExcel Building Blocks (biobb)

Based on the official GROMACS tutorial.

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This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).

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Settings

Biobb modules used

• biobb_io: Tools to fetch biomolecular data from public databases.
• biobb_model: Tools to model macromolecular structures.
• biobb_gromacs: Tools to setup and run Molecular Dynamics simulations.
• biobb_analysis: Tools to analyse Molecular Dynamics trajectories.

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.
• 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_md_setup.git
cd biobb_wf_md_setup
conda env create -f conda_env/environment.yml
conda activate biobb_GMX_MDsetup_tutorial
jupyter nbextension enable python-markdown/main
jupyter-notebook biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb

Please execute the following commands before launching the Jupyter Notebook if you experience some issues with widgets such as NGL View (3D molecular visualization):

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

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Tutorial

Click here to view tutorial in Read the Docs

Click here to execute tutorial in Binder

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Version

2023.1 Release

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).

• (c) 2015-2023 Barcelona Supercomputing Center
• (c) 2015-2023 Institute for Research in Biomedicine

Licensed under the Apache License 2.0, see the file LICENSE for details.