Difference between revisions of "2016 AMBER tutorial with Thrombin"

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===MM-GBSA Energy Calculation===
===MM-GBSA Energy Calculation===
==V. Frequently Encountered Problems==
==V. Frequently Encountered Problems==

Latest revision as of 14:16, 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, Beilei

IV. Simulation Analysis


Lauren, Haoyue

MM-GBSA Energy Calculation


V. Frequently Encountered Problems