Tutorials for Preparing the Trypsin/Benzamidine System

This tutorial walks through the process of preparing, parametrizing, equilibrating, and generating the starting structures for a SEEKR2 calculation of the trypsin/benzamidine system.

This tutorial requires OpenMM and AmberTools to be installed and ready to run.

A structure of benzamidine bound to the trypsin protein.

Contents:

• Tutorial: Parametrizing the Trypsin/Benzamidine System
• Tutorial: Generating Trypsin/Benzamidine Starting Structures With HIDR