The input files for the alchemical binding free energy simulations with AToM v3.2.1 for the publication Taming Multiple Binding Poses in Alchemical Binding Free Energy Prediction: the β-cyclodextrin Host-Guest SAMPL9 Blinded Challenge by Sheenam Khuttan, Solmaz Azimi, Joe Z. Wu, Sebastian Dick, Chuanjie Wu, Huafeng Xu, Emilio Gallicchio.
The work is also presented here
poses/ Initial structures of each pose of each complex
ABFE/ Absolute binding free energy calculations for the G1 ligand to the bCD and mCD hosts
RBFE1/ Relative binding free energy calculations from G1 to PHM and from PHM to PMZ
RBFE2/ Relative binding free energy calculations from PMZ to the other guests