System Setup for AToM Calculations
Since it does not require alchemical topologies, preparing protein-ligand systems for AToM is essentially the same as for standard molecular dynamics. Granted, preparing protein-ligand complexes for molecular dynamics is not always straightforward. AToM does not make the job any easier or significantly more difficult. This section will not teach you how to properly prepare a molecular system. We will focus only on the aspects that are specific to AToM:
The binding site definition
The ligand displacement
The ligand alignment restraints
There are aspects specific to absolute binding free energy estimation (ABFE) and aspects specific to relative binding free energy estimation (RBFE). We will assume ABFE to start and go from there.
Binding Site Definition
Like any other calculation, a binding free energy calculation starts by defining the object of the calculation. In alchemical binding free energy calculations, this is the complex between a ligand and a receptor. More specifically, we need to specify the set of configurations of the protein-ligand system that we call a "complex." In AToM, this is commonly accomplished by restraining the ligand within a spherical region around the receptor binding site. Doing so prevents the ligand from wandering away from the receptor when it is not coupled to it. This step also has the more profound significance of defining the standard state of the binding equilibrium. The results of absolute binding free energy (ABFE) calculations are meaningless unless the binding site is properly defined.
While it is still required in theory, the definition of the binding site is less of a concern for most relative binding free energy (RBFE) calculations. If the ligands in the pair are strong binders, they are unlikely to leave the binding site even if they are not restrained to it. In these cases, it is relatively safe to skip the definition of the binding site. (If you do not add binding site restraints and see one of the ligands leave the binding site, it is safe to assume that the ligand in question is a non-binder.)
Example of the definition of the binding site of the Estrogen Receptor α. The center of the binding site (blue ball) is the center of mass of the chosen Cα atoms (gray balls). The reference atom of the ligand (gree ball) is restrained within the yellow circle.