gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS

TLDR

Molecular mechanics/Poisson–Boltzmann (Generalized‑Born) surface area is a widely used method for estimating binding free energies that balances accuracy and computational efficiency, especially for large systems, and has spurred the development of several GROMACS‑compatible programs. gmx_MMPBSA provides users with a broad set of options—including PB, GB, or 3D‑RISM solvation models, stability calculations, computational alanine scanning, entropy corrections, binding free‑energy decomposition, and advanced techniques such as variable‑dielectric alanine scanning and interaction entropy—while integrating auxiliary tools for testing and analysis. The tool overcomes limitations of existing programs and improves usability through the integrated gmx_MMPBSA_test and gmx_MMPBSA_ana utilities, which supply illustrative examples and streamlined graphical outputs. The latest version (v1.4.3, 26/05/2021) is freely available with documentation, test files, and tutorials at https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA.

Abstract

Molecular mechanics/Poisson–Boltzmann (Generalized-Born) surface area is one of the most popular methods to estimate binding free energies. This method has been proven to balance accuracy and computational efficiency, especially when dealing with large systems. As a result of its popularity, several programs have been developed for performing MM/PB(GB)SA calculations within the GROMACS community. These programs, however, present several limitations. Here we present gmx_MMPBSA, a new tool to perform end-state free energy calculations from GROMACS molecular dynamics trajectories. gmx_MMPBSA provides the user with several options, including binding free energy calculations with different solvation models (PB, GB, or 3D-RISM), stability calculations, computational alanine scanning, entropy corrections, and binding free energy decomposition. Noteworthy, several promising methodologies to calculate relative binding free energies such as alanine scanning with variable dielectric constant and interaction entropy have also been implemented in gmx_MMPBSA. Two additional tools—gmx_MMPBSA_test and gmx_MMPBSA_ana—have been integrated within gmx_MMPBSA to improve its usability. Multiple illustrating examples can be accessed through gmx_MMPBSA_test, while gmx_MMPBSA_ana provides fast, easy, and efficient access to different graphics plotted from gmx_MMPBSA output files. The latest version (v1.4.3, 26/05/2021) is available free of charge (documentation, test files, and tutorials included) at https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA.