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_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.
- jupyter: Free software, open standards, and web services for interactive computing across all programming languages.
- nglview: Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
- plotly: Python interactive graphing library integrated in Jupyter notebooks.
- simpletraj: Lightweight coordinate-only trajectory reader based on code from GROMACS, MDAnalysis and VMD.
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_wf_protein-complex_md_setup
jupyter-notebook biobb_wf_protein-complex_md_setup/notebooks/biobb_wf_protein-complex_md_setup.ipynbClick here to view tutorial in Read the Docs
Click here to execute tutorial in Binder
Click here to open tutorial in Google Colab
2024.1
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) 2015-2024 Barcelona Supercomputing Center
- (c) 2015-2024 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
