2016 AMBER tutorial with Thrombin

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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

II. Structural Preparation

Antechamber, Parmchk, tLeap

III. Simulation using pmemd


IV. Simulation Analysis


MM-GBSA Energy Calculation

V. Frequently Encountered Problems