Difference between revisions of "2016 AMBER tutorial with Thrombin"

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Agatha, Haoyue
==IV. Simulation Analysis==
==IV. Simulation Analysis==

Revision as of 14:15, 6 April 2016

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

Omar, Katie

III. Simulation using pmemd


Agatha, Haoyue

IV. Simulation Analysis


MM-GBSA Energy Calculation

V. Frequently Encountered Problems