Tutorial – Protein-Complex MD Setup with Jupyter Notebooks and BioBB.

Trainer: Adam Hospital

Overview: 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). This particular example is the T4 lysozyme L99A/M102Q protein, in complex with 2-propylphenol.

Learning outcomes

By the end of this session you will be able to:

• Design and run a complete workflow for a molecular dynamics simulation using BioBB
• Visualise PDB structures using NGL
• Use BioBB to plot graphs of your results
• Use auxiliar libraries to support your simulation workflow

Materials

• Link to the BioBB tutorial