2023 AMBER tutorial 1 with PDBID 4S0V
Contents
Introduction
AMBER is a molecular dynamics program that can be run on your protein/ligand complex to ensure that the interactions between the two structures are stable. DOCK shows us how the two interact with each other at one point in time. AMBER looks at those interactions over time to ensure that forces will not occur which will push the ligand out of the binding site as the complex naturally moves. Before starting the analysis it's best to download a new protein/ligand complex from the PDB and isolate the protein structure. Follow the steps in the *[1] tutorial to do this.
Setting Up Your Environment
Just as with DOCK you should set up for directory structure at this point to keep everything organized and easy to find. We will be creating a new structure which looks like:
