OpenGBSA Manual¶
OpenGBSA is a high-performance computational chemistry toolkit for estimating the relative binding free energies of protein-ligand and protein-protein complexes. It implements the MM/GBSA (Molecular Mechanics / Generalized Born Surface Area) method using OpenMM for rapid processing on CPUs and GPUs.
Designed for both ease of use and scientific rigor, OpenGBSA automates the complex workflows of topology preparation, trajectory processing, and energy decomposition.
Installation guide and quickstart tutorial.
Detailed instructions on configuration, input structures, and output interpretation.
Five worked examples, one per receptor/ligand combination and input format, each runnable end-to-end from the repository.
Rigorous mathematical background, GB model definitions (OBC2, GBn), and entropy methods.
Python API documentation for custom workflows and integration.
Table of Contents¶
Introduction
Tutorials
Theory and Methods
Citing OpenGBSA¶
If you use OpenGBSA in your research, please cite:
OpenGBSA: see CITATION.cff in the repository root for citation metadata.
OpenMM: Eastman, P., et al. (2017). OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLoS Computational Biology, 13(7), e1005659.
MDTraj: McGibbon, R. T., et al. (2015). MDTraj: A modern open library for the analysis of molecular dynamics trajectories. Biophysical Journal, 109(8), 1528-1532.