Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb) (jupyter notebook)

Version 1

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).

Workflow engine is a jupyter notebook. It can be run in binder, following the link given, or locally. Auxiliar libraries used are: nb_conda_kernels, nglview, ipywidgets, os, plotly, and simpletraj. Environment can be setup using the included environment.yml file.