Fast parametrization of Martini3 models for fragments and small molecules repository

Here, we introduce the data repository of Auto-MartiniM3, an advanced and updated version of the Auto-Martini program, designed to automate the coarse-graining of small molecules to be used with the Martini 3 force field. We validated our approach by modeling 81 small molecules from the Martini Database and comparing their water-oil partitionning behavior during solvation free energy simulations with ones obtained from models designed by Martini experts. - simulation and TI computation results, as well as coarse-grain parametrizations created with Auto-MartiniM3 are avaliable in TI_simulations.zip Additionally, we assessed the behavior of Auto-MartiniM3-generated models by calculating solute translocation and free energy across lipid bilayers. Computation and simulation data are available in PMF_simulations.zip and Auto-MartiniM3-made models (with some manually introduced changes for increasing stability) are available in PMF_molecules.zip We also evaluated Auto-MartniM3-made caffeine model by testing its binding to the adenosine A2A receptor.Simulation data are available in A2A_POPC_AM3caffeine.zip Auto-MartiniM3 source code is freely available at https://github.com/Martini-Force-Field-Initiative/Automartini_M3