2012 AMBER Tutorial with Biotin and Streptavidin

For additional Rizzo Lab tutorials see AMBER Tutorials.

In this tutorial, we will learn how to run a molecular dynamics simulation of a protein-ligand complex. We will then post-process that simulation by calculating structural fluctuations (with RMSD) and free energies of binding (MM-GBSA).

Introduction

Biotin and Streptavidin

For information of the Biotin and Streptavidin system, see 2012 DOCK tutorial with Streptavidin