2015 AMBER tutorial with PARP

From Rizzo_Lab
Revision as of 14:20, 1 April 2015 by Fochtman (talk | contribs) (Created page with " 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 ...")
(diff) ←Older revision | view current revision (diff) | Newer revision→ (diff)
Jump to: navigation, search

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

Preparing the ligand and receptor in Chimera

Antechamber

III. Simulation using sander

Minimization

Production

IV. Simulation Analysis

Checking Output Files

Ptraj

MM-GBSA Energy Calculation

V. Frequently Encountered Problems