2023 AMBER tutorial 1 with PDBID 4S0V

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Introduction

AMBER is a molecular dynamics program that can be run on your final molecular structure to ensure that it's stable and is actually bound to the protein. Before starting the analysis it's best to download a new protein/ligand complex from the PDB. Follow the steps in the


Setting Up Your Environment

Force Field Generation

TLeap Implemenation

Complex Minimization and Equilibration