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).

I. Introduction

Yaping

II. Structural Preparation

Antechamber, Parmchk, tLeap

Omar, Katie

III. Simulation using pmemd

PMEMD

Agatha, Beilei

IV. Simulation Analysis

Ptraj

Lauren, Haoyue