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AMBER Protein MD Setup tutorials using BioExcel Building Blocks (biobb)

Based on the official GROMACS tutorial.

This tutorials aim to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) wrapping the Ambertools MD package.

Settings

Biobb modules used

  • biobb_io: Tools to fetch biomolecular data from public databases.
  • biobb_amber: Tools to setup and run Molecular Dynamics simulations using the Ambertools MD package.
  • biobb_analysis: Tools to analyse Molecular Dynamics trajectories.
  • biobb_structure_utils: Tools to modify or extract information from a PDB structure file.
  • biobb_chemistry: Tools to to perform chemical conversions.

Auxiliary libraries used

  • jupyter: Free software, open standards, and web services for interactive computing across all programming languages.
  • plotly: Python interactive graphing library integrated in Jupyter notebooks.
  • nglview: Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
  • simpletraj: Lightweight coordinate-only trajectory reader based on code from GROMACS, MDAnalysis and VMD.
  • gfortran: Fortran 95/2003/2008/2018 compiler for GCC, the GNU Compiler Collection.
  • libgfortran5: Fortran compiler and libraries from the GNU Compiler Collection.

Conda Installation

git clone https://github.com/bioexcel/biobb_wf_amber.git
cd biobb_wf_amber
conda env create -f conda_env/environment.yml
conda activate biobb_wf_amber

Launch

Protein MD Setup tutorial

jupyter-notebook biobb_wf_amber/notebooks/md_setup/biobb_wf_amber_md_setup.ipynb

Protein-Ligand Complex MD Setup tutorial

jupyter-notebook biobb_wf_amber/notebooks/md_setup_lig/biobb_wf_amber_md_setup_lig.ipynb

Constant pH MD Setup tutorial

jupyter-notebook biobb_wf_amber/notebooks/md_setup_ph/biobb_wf_amber_md_setup_ph.ipynb

ABC MD Setup tutorial

jupyter-notebook biobb_wf_amber/notebooks/abc_setup/biobb_wf_amber_abc_setup.ipynb

Tutorials

Click here to view tutorials in Read the Docs

Version

2024.1 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).

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