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.
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.
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.
git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git cd biobb_wf_amber_md_setup conda env create -f conda_env/environment.yml conda activate biobb_AMBER_MDsetup_tutorials ./conda_env/post-link.sh
Protein MD Setup tutorial
Protein-Ligand Complex MD Setup tutorial
Constant pH MD Setup tutorial
ABC MD Setup tutorial
Copyright & Licensing
Licensed under the Apache License 2.0, see the file LICENSE for details.