2015 AMBER tutorial with PARP
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).
- 1 I. Introduction
- 2 II. Structural Preparation
- 3 III. Simulation using sander
- 4 IV. Simulation Analysis
- 5 V. Frequently Encountered Problems