Tutorials

Basics

• bALA Tutorial

A simple, step-by-step tutorial on how to load a basic MM system, perform geometry optimization, and scan a simple reaction coordinate.

• Modeling a simple SN2 reaction

• Simple hybrid QC/MM system

• Umbrella Sampling

• Simple Enzyme Reaction (TIM).

This video tutorial uses the classic example of the enzyme Triose Phosphate Isomerase (TIM) to cover the following aspects: how to load a system, edit/reduce the number of atoms (pruning), energy minimization, selection of a QC region, and the scan of the first step of the catalytic cycle.

Case Studies

Chorismate Mutase

In this series of tutorials, we will explore the reaction catalyzed by the enzyme chorismate mutase (CM), with a particular focus on various sampling and analysis strategies. Special thanks to Dr. Atsu Agbaglo and Professor Nathan DeYonker from the University of Memphis for their assistance with the original files and valuable suggestions.

• Modeling the CM reaction using PES scan

• Modeling the CM reaction using NEB

• Calculating free energy by umbrella sampling (US)

Combining pDynamo3 scripts and EasyHydrid interface

• Combining pDynamo3 scripts and EasyHydrid interface.