Repository of Auto-MartiniM3: Fast parametrization of Martini3 models for fragments and small molecules
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 and Auto-MartiniM3-made models (with some manually introduced changes for increasing stability) are available in PMF_simulations.zip We evaluated Auto-MartniM3-made caffeine model by testing its binding to the adenosine A2A receptor. Simulation data are available in A2A_POPC_AM3caffeine.zip To confirm applicability of Auto-MartiniM3 as the tool for high-throughput coarse grain parametrization, we deployed it on 100 000 molecules from Enamine Fragment Collection (files avaliable in Enamine100k_parametrization.zip) and simulated 23619 ligands in a box of water (simulation results are avaliable in Enamine24k_simulations.zip). Auto-MartiniM3 source code is freely available at https://github.com/Martini-Force-Field-Initiative/Automartini_M3
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@misc{https://doi.org/10.5281/zenodo.15783891,
doi = {10.5281/ZENODO.15783891},
url = {https://zenodo.org/doi/10.5281/zenodo.15783891},
author = {Szczuka, Magdalena and P. Pereira, Gilberto and Walter, Luis and Guéroult, Marc and Poulain, Pierre and Bereau, Tristan and Telles de Souza, Paulo Cesar and Chavent, Matthieu},
keywords = {martini3ff, gromacs, Molecular Dynamics Simulation},
title = {Repository of Auto-MartiniM3: Fast parametrization of Martini3 models for fragments and small molecules},
publisher = {Zenodo},
year = {2025},
copyright = {Creative Commons Attribution 4.0 International}
}