Tutorials

Basics

• Loading and pruning system

• Simple hybrid QC/MM system

• Geometry optimization

• Modeling a simple SN2 reaction

• Umbrella Sampling

• Simple Enzyme Reaction (TIM).

Case Studies

Chorismate Mutase

In this series of tutorials, we will delve into the investigation of the reaction catalyzed by the enzyme chorismate mutase (CM), with a particular emphasis on exploring various sampling and analysis strategies. Special thanks to Atsu Agbaglo and Professor Nathan DeYonker, University of Memphis, for help with the original files and 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.