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Updated: May 28, 2026

Online Size-exclusion and Ion-exchange Chromatography on a SAXS Beamline

Online Size-exclusion and Ion-exchange Chromatography on a SAXS Beamline

Published on: January 5, 2017

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

Jiaxing Zhang¹, Tao Gu², Chuanxi Li³

¹State Key Laboratory of Chemical Engineering and Low-Carbon Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.

Molecules (Basel, Switzerland)

|May 27, 2026

Summary

This summary is machine-generated.

We developed s_mmpbsa, a user-friendly, cross-platform tool for Molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) calculations. This enhances binding energy estimation accuracy and performance for molecular dynamics simulations in Gromacs.

Keywords:

MM-PBSA binding energy electrostatic screening interaction entropy molecular dynamics molecular interactions

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Area of Science:

Computational chemistry
Molecular modeling
Biophysics

Background:

Molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) is crucial for estimating binding energies.
Existing MM-PBSA programs often require Linux and lack cross-platform compatibility.
Gromacs is a widely used software for molecular dynamics (MD) simulations.

Purpose of the Study:

To introduce s_mmpbsa, a lightweight, cross-platform MM-PBSA program.
To enable MM-PBSA calculations on native Windows systems without requiring a subsystem.
To improve the accuracy and performance of binding energy calculations from MD simulations.

Main Methods:

Developed s_mmpbsa, incorporating electrostatic screening and interaction entropy.
Validated accuracy using HIV-1 protease inhibitor complexes.
Compared performance against g_mmpbsa under identical conditions.

Main Results:

s_mmpbsa demonstrates improved binding free energy calculation accuracy.
The program offers enhanced performance compared to g_mmpbsa.
Successful validation on HIV-1 protease inhibitor complexes.

Conclusions:

s_mmpbsa provides an efficient and practical solution for calculating interaction energies from Gromacs MD simulations.
The tool supports molecular design applications like computational enzyme design and molecular screening.
Offers valuable protocols for researchers on native Windows platforms.