s_mmpbsa: A Lite and Cross-Platform MM-PBSA Program
4 affiliations
- 1State Key Laboratory of Chemical Engineering and Low-Carbon Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- 2School of Engineering, Westlake University, Hangzhou 310014, China
- 3Petrochemical Research Institute, PetroChina, Beijing 102206, China
- 4Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, China
Abstract
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.
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BibTeX
@article{zhang2026smmpbsa,
title = {{s_mmpbsa: A Lite and Cross-Platform MM-PBSA Program}},
author = {J C Zhang and Tao Gu and Chuanxi Li and Wei Qi},
journal = {Molecules},
year = {2026},
month = may,
doi = {10.3390/molecules31101683},
url = {https://doi.org/10.3390/molecules31101683},
note = {CC BY},
}
RIS
TY - JOUR
TI - s_mmpbsa: A Lite and Cross-Platform MM-PBSA Program
AU - J C Zhang
AU - Tao Gu
AU - Chuanxi Li
AU - Wei Qi
PY - 2026
DA - 2026/05/15
JO - Molecules
DO - 10.3390/molecules31101683
UR - https://doi.org/10.3390/molecules31101683
AB - 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.
SN - 1420-3049
SN - 1433-1373
ER -