Protein 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, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).
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
Click here to view tutorial in Read the Docs
Click here to execute tutorial in Binder
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.