2023 AMBER tutorial 3 with PDBID 2P16

Introduction

Howdy! If you've gotten this far with your MD project, you've now moved out of the realm of DOCK6 and into the world of molecular dynamics (MD). This tutorial will cover how to use the AMBER 16 software package to simulate your protein-ligand complex on a sub-microsecond timeframe and use the resulting data to calculate binding energies.

Preparing the Structure

Before you start any preparation, you need to keep yourself organized to make sure that you're running the right files and jobs for your MD simulation, otherwise, it may explode.

To do this, you can either copy the example AMBER directory to your scratch directory (this may change per year):

/gpfs/projects/AMS536/2023

Or, you can create the following directories:

mkdir 000.parameters
mkdir 001.tleap_build
mkdir 002.equilibration
mkdir 003.production
mkdir 004.analysis
mkdir zzz.master

For this tutorial, we will be copying the example AMBER setup into our folder to run our complex.