s_mmpbsa: A Lite and Cross-Platform MM-PBSA Program

Molecular mechanics/the Poisson-Boltzmann surface area (MM-PBSA) is a popular method for binding energy estimation. Several programs have been developed for performing MM-PBSA calculations in conjunction with Gromacs, the most popular molecular dynamics (MD) software. However, current programs are limited to Linux-based systems and lack cross-platform usability. To address this, we present s_mmpbsa, a lite and cross-platform MM-PBSA program, to support binding energy calculation on native Windows platforms without a subsystem. By incorporating electrostatic screening and interaction entropy, s_mmpbsa achieves improved binding free energy calculation accuracy, validated on a dataset of HIV-1 protease inhibitor complexes. In addition, s_mmpbsa achieves enhanced performance with g_mmpbsa in the same parameters and conditions. Indeed, s_mmpbsa offers an efficient and practical solution for interaction energy calculation from MD simulations in Gromacs, providing valuable protocols for further molecular design applications such as computational enzyme design and molecular screening.