Use outputs of Docking for FEP

This document describes how to use the outputs of Docking as inputs to FEP tools.

Assumptions

We assume that you have

1. created a Complex object
2. run Docking

Pick poses to use

If you have used docking on a number of ligands, you can find the best poses for each ligand using:

poses = sim.docking.get_poses()
poses = poses.filter_top_poses()

These poses can then be used as ligands:

sim.ligands = poses

and ABFE can be run on them as described here