BOSS
Biochemical and Organic Simulation System
Computing Applications (HPC) Academic free / commercial required (Partial)
About
Molecular modeling for MM, Metropolis Monte Carlo simulations, and semiempirical quantum mechanics to study organic and biomolecular systems. Used for energy minimizations, conformational searching, and calculating free energies of solvation and binding using the OPLS force fields.
Key Features
- Force fields: OPLS-AA, OPLS/CM1A
- Methods: Monte Carlo, minimization
- Free energy: FEP, TI calculations
- Solvation: explicit, GB/SA continuum
Skills
MCP skills available for BOSS, callable from AI workflows and the Paramus chat:
- Am1 — Run AM1 semi-empirical calculation. Fast quantum mechanical calculation using the AM1 method for electronic properties.
- Calculation Info — [info-only, does not execute] Documentation
- Changelog — Get BOSS module version history and changes.
- Conformer Search — Run conformational search. Systematically explores molecular conformational space to find low-energy conformers.
- Gbsa Optimize — Run GBSA solvation optimization. Optimizes molecular geometry with implicit solvation using Generalized Born Surface Area model.
- Info — Get BOSS module information and capabilities.
- Kernel Execute — Execute command in BOSS shell session.
- Kernel List — List active BOSS shell sessions.
- Kernel Start — Start interactive shell session in BOSS Docker container.
- Kernel Stop — Stop BOSS shell session.
- Methods — Get list of available BOSS RPC methods.
- Opls Info — [info-only, does not execute] BRAIN operation: BOSS OPLS optimization
- Opls Optimize — Run OPLS force field optimization. Optimizes molecular geometry using the OPLS-AA force field for organic molecules and drug-like compounds.
- Pm3 — Run PM3 semi-empirical calculation. Fast quantum mechanical calculation using the PM3 method for electronic properties.
- Search Info — [info-only, does not execute] BRAIN operation: BOSS conformational search
- Semiempirical Info — [info-only, does not execute] BRAIN operation: BOSS semiempirical calculations
- Simulation Info — [info-only, does not execute] Documentation
- Version — Get BOSS program version from Docker container.
Browse the full BOSS skill documentation
Free for academic use. Commercial license required for for-profit use.
Citation
Jorgensen, W.L.; Tirado-Rives, J. Molecular modeling of organic and biomolecular systems using BOSS and MCPRO. J. Comput. Chem. 26, 1689-1700 (2005). DOI:10.1002/jcc.20297
Frequently Asked Questions
What is BOSS?
BOSS is a computing applications (hpc) application available in the Paramus App Store. Molecular modeling for MM, Metropolis Monte Carlo simulations, and semiempirical quantum mechanics to study organic and biomolecular systems. Used for energy minimizations, conformational searching, and calculating free energies of solvation and binding using the OPLS force fields.
Is BOSS free to use?
Yes. BOSS is distributed under the Academic free / commercial required (Partial) license and is available at no cost through the Paramus App Store.
How do I install BOSS?
BOSS is installed through Paramus Chemistry OS, an on-premise Windows platform for computational chemistry. Open the Paramus App Store in your local installation and select BOSS for one-click deployment.
What are the key features of BOSS?
Key features of BOSS include: Force fields: OPLS-AA, OPLS/CM1A; Methods: Monte Carlo, minimization; Free energy: FEP, TI calculations; Solvation: explicit, GB/SA continuum.
What type of application is BOSS?
BOSS belongs to the “Computing Applications (HPC)” category in the Paramus App Store. It runs on Paramus Chemistry OS and can also be accessed through Paramus Cloud for supported workflows.
What platform does BOSS run on?
BOSS runs on Paramus Chemistry OS, a Windows-based on-premise platform that provides local compute power for demanding simulations. It requires a Paramus OS installation with appropriate hardware resources.
Can BOSS be automated or integrated with AI workflows?
Yes. BOSS is available as part of the Paramus ecosystem which supports MCP (Model Context Protocol) tools for AI-driven automation. This enables integration with large language models and automated research pipelines.
How should I cite BOSS in publications?
The recommended citation for BOSS is: Jorgensen, W.L.; Tirado-Rives, J. Molecular modeling of organic and biomolecular systems using BOSS and MCPRO. J. Comput. Chem. 26, 1689-1700 (2005). DOI:10.1002/jcc.20297