Difference between revisions of "2015 AMBER tutorial with PARP"

Revision as of 14:21, 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

AMBER

Organizing Directories

II. Structural Preparation

Antechamber

III. Simulation using sander

Minimization

Production

IV. Simulation Analysis

Ptraj

MM-GBSA Energy Calculation

V. Frequently Encountered Problems