2016 AMBER tutorial with Thrombin
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).
II. Structural Preparation
Antechamber, Parmchk, tLeap
III. Simulation using pmemd