2021 AMBER tutorial 1 with PDBID 1HW9
In this tutorial, we'll be exploring the wonders of molecular dynamics through the use of AMBER 16. AMBER 16 we'll help study the binding characteristics of the ligand to the target protein!
It's important to stay organized during this process as we'll be generating a number of files during the process. Overall, we'll be working within five directories. They should be created as follows:
mkdir 001_structure mkdir 002_parameters mkdir 003_leap mkdir 004_equil mkdir 005_production
Before proceeding, double-check that all directories have correctly been made.