Defining RBFE Calculations

An AlchemicalNetwork for relative binding free energy calculations can be easily created with a RBFEAlchemicalNetworkPlanner.

Creating the AlchemicalNetwork basically involves the following three steps:

1. Creating a LigandNetwork to represent the planned ligand transformations.

2. Creating a ChemicalSystem (which combines protein, solvent, and ligand) for each ligand.

3. Using the LigandNetwork to create the AlchemicalNetwork (where each node is a ChemicalSystem and the edges also carry information about the Protocol).

Each aspect of this can be performed manually. For details on customizing the LigandNetwork, see Defining the Ligand Network.