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_Protein-Complex_MDsetup_tutorial
jupyter-notebook biobb_wf_protein-complex_md_setup/notebooks/biobb_Protein-Complex_MDsetup_tutorial.ipynbClick here to view tutorial in Read the Docs
Click here to execute tutorial in Binder
2023.3
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.
