(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Dwight Mcgee, Bill Miller III, and Jason Swails 2009

AMBER ADVANCED TUTORIALS
TUTORIAL 3

Python Script MMPBSA.py

Dwight McGee, Bill Miller III, & Jason Swails

In this tutorial we will demonstrate the use of the MM-PBSA method as released in AmberTools to calculate binding free energy, run alanine scanning, and calculate normal modes for entropy calcalations. The tutorial is broken down as follows:

• Section 3.1 : Calculate the binding free energy of a protein-protein complex (Ras-Raf).

• Section 3.2 : Calculate the binding free energy of a protein-ligand complex (Estrogen Receptor and Raloxifene).

• Section 3.3 : Calculate the binding free energy of Ras-Raf and use Alanine Scanning to compare to the binding energy of a mutant Ras-Raf complex that has had a residue mutated to alanine and analyze the results.

• Section 3.4 : Calculate the binding free energy of Ras-Raf in parallel using three processors.

• Section 3.5 : Calculate the entropy of the Estrogen Receptor and Raloxifene complex using Normal Mode Analysis (Nmode).

• Section 3.6 : Decomposing the free energy contributions to the binding free energy of Ras-Raf in a per-residue or pairwise per-residue basis.

CLICK HERE TO GO TO SECTION 3.1

CLICK HERE TO RETURN TO THE INTRODUCTION

(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Dwight McGee, Bill Miller III, and Jason Swails