The accurate study of the binding mechanism of a ligand to its molecular target is fundamental to discover new possible drug targets. In order to do that, we can employ free-energy calculations due to their accuracy, although the lack in user-friendliness generally hampers their broad application. In this regard, the Funnel-Metadynamics Advanced Protocol (FMAP) represents a flexible and user-friendly protocol to perform Funnel-Metadynamics, a binding free-energy method that employs a funnel-shape restraint potential to obtain the ligand binding mode and the accurate calculation of the absolute ligand/protein binding free energy. Through the use of graphical interfaces, FMAP is able to assist the user during all steps of the investigation, allowing to disclose the ligand binding mode and mechanism and accurately compute the absolute protein/ligand binding free energy. This package contains inputs and outputs files of FMAP produced for the paradigmatic benzamidine-trypsin system.

We would like to acknowledge the support of the Italian MIUR-PRIN 2017 (project id 2017FJZZRC) and the Swiss National Supercomputing Centre (CSCS) [project ID u8].