Merging Topologies for Relative Binding Free Energies

Zeke A. Piskulich¹, Patricio Barletta¹, Ryan Snyder¹, and Darrin M. York¹

¹Laboratory for Biomolecular Simulation Research, Institute

for Quantitative Biomedicine and Department of Chemistry and Chemical

Biology, Rutgers University, Piscataway, NJ 08854, USA

Learning objectives

Learn how to merge topologies for Relative Binding Free Energy simulations

Activity

Merging Topologies

One of the most challenging stages for setting up an RBFE calculation by hand is to generate merged topologies for each endstate. Though at a particular end-state one ligand is fully turned off, both ligands must be present so that they can share a common core.