2015 AMBER tutorial with PARP

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

Amber - Assisted Model Building with Energy Refinement - is a multi-program suite for macromolecular simulations. Amber14 is the most recent version of the software and it includes new force fields such as ff14SB. In addition, in this release, more features from sander have been added to pmemd for both CPU and GPU platforms, including performance improvements, and support for extra points, multi-dimension replica exchange, a Monte Carlo barostat, ScaledMD, Jarzynski sampling, explicit solvent constant pH, GBSA, and hydrogen mass repartitioning. Support is also included for the latest Kepler, Titan and GTX7xx GPUs expanded options for Poisson-Boltzmann solvation calculations, accelerated molecular dynamics, additional features in sander pmemd code, and expanded methods for free energy calculations. Our lab is set up with Amber14 and the latest update of AmberTools14 which contains the programs such as antechamber and tleap to set up your simulation.

The [1] is available to get started with using Amber14. You can search the document for keywords such as "tleap" if you use Adobe Acrobat to view the file. Additionally, [2] is another reference for the programs available under Amber tools.