Difference between revisions of "2016 AMBER tutorial with Thrombin"
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==I. Introduction== | ==I. Introduction== | ||
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| + | Yaping | ||
==II. Structural Preparation== | ==II. Structural Preparation== | ||
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====Antechamber, Parmchk, tLeap==== | ====Antechamber, Parmchk, tLeap==== | ||
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| + | Omar, Katie | ||
==III. Simulation using pmemd== | ==III. Simulation using pmemd== | ||
====PMEMD==== | ====PMEMD==== | ||
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| + | Agatha, Beilei | ||
==IV. Simulation Analysis== | ==IV. Simulation Analysis== | ||
===Ptraj=== | ===Ptraj=== | ||
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| + | Lauren, Haoyue | ||
===MM-GBSA Energy Calculation=== | ===MM-GBSA Energy Calculation=== | ||
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| + | Monaf | ||
==V. Frequently Encountered Problems== | ==V. Frequently Encountered Problems== | ||
Latest revision as of 13:16, 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).
Contents
I. Introduction
Yaping
II. Structural Preparation
Antechamber, Parmchk, tLeap
Omar, Katie
III. Simulation using pmemd
PMEMD
Agatha, Beilei
IV. Simulation Analysis
Ptraj
Lauren, Haoyue
MM-GBSA Energy Calculation
Monaf
