Difference between revisions of "2015 AMBER tutorial with PARP"

From Rizzo_Lab
Jump to: navigation, search
(III. Simulation using sander)
(III. Simulation using pmemd)
Line 17: Line 17:
==III. Simulation using pmemd==
==III. Simulation using pmemd==
=== Minimization ===
=== Production ===
==IV. Simulation Analysis==
==IV. Simulation Analysis==

Revision as of 14:24, 1 April 2015

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


Organizing Directories

II. Structural Preparation

Antechamber, Parmchk, tLeap

III. Simulation using pmemd

IV. Simulation Analysis


MM-GBSA Energy Calculation

V. Frequently Encountered Problems