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_gromacs: 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 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
Tutorial¶
Click here to view tutorial in Read the Docs
Version¶
2023.3
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.