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Protein MD Setup tutorial using BioExcel Building Blocks (biobb) through REST API

Based on the official GROMACS tutorial.

This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks (biobb) REST API. The particular example used is the Lysozyme protein (PDB code 1AKI).

Settings

Auxiliar libraries used

  • requests: Requests allows you to send organic, grass-fed HTTP/1.1 requests, without the need for manual labor.
  • 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.

Conda Installation and Launch

git clone https://github.com/bioexcel/biobb_wf_md_setup_api.git
cd biobb_wf_md_setup_api
conda env create -f conda_env/environment.yml
conda activate biobb_MDsetupAPI_tutorial
jupyter-nbextension enable --py --user widgetsnbextension
jupyter-nbextension enable --py --user nglview
jupyter-notebook biobb_wf_md_setup_api/notebooks/biobb_MDsetupAPI_tutorial.ipynb

Tutorial

Click here to view tutorial in Read the Docs

Click here to execute tutorial in Binder

Version

May 2020 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.