(1c) Design Problems with Biomolecules

This session will highlight tools, tips, and trouble-shooting biomolecular simulations. We will introduce CharmGUI, Glycam.org, Amber Leap, and H++, which are popular tools to build protein, lipid, and/or carbohydrate-based systems with appropriate protonation states, end groups, etc. We will also discuss force fields parametrized specifically for these systems as well as what to do when your ligand is not included in the force field. We will share how we diagnosed and corrected errors in creating several biomolecular systems. Last, we will practice extracting knowledge from biomolecular simulations, determining driving forces in thermodynamically-driven processes.