AmberTools
Computing Applications (HPC) GPL-2.0 (Free)
About
A force field parameterization and molecular dynamics preparation suite providing antechamber for GAFF/GAFF2 atom typing, tleap for building simulation systems, cpptraj for trajectory analysis, and reduce for hydrogen optimization.
Key Features
- Parameterization: antechamber, parmchk2
- System building: tleap, xleap
- Analysis: cpptraj, pytraj
- Force fields: GAFF, GAFF2, ff19SB
Skills
MCP skills available for AmberTools, callable from AI workflows and the Paramus chat:
- Antechamber — API v1.2: Generate force field parameters with Antechamber.
- Capabilities — Get AmberTools capabilities and supported features
- Changelog — Get AmberTools module version history and changes
- Cpptraj — API v1.2: Analyze trajectory with cpptraj.
- Info — Get AmberTools module information and capabilities
- Kernel Execute — Execute command in AmberTools shell session
- Kernel List — List active AmberTools shell sessions
- Kernel Start — Start interactive shell session in AmberTools Docker container
- Kernel Stop — Stop AmberTools shell session
- Methods — Get list of available AmberTools RPC methods
- Tleap — API v1.2: Prepare simulation system with tLEaP.
- Version — Get AmberTools program version from Docker container
Browse the full AmberTools skill documentation
Citation
Case, D.A. et al. AmberTools. J. Chem. Inf. Model. 63, 6183-6191 (2023). DOI:10.1021/acs.jcim.3c01153
Frequently Asked Questions
What is AmberTools?
AmberTools is a computing applications (hpc) application available in the Paramus App Store. A force field parameterization and molecular dynamics preparation suite providing antechamber for GAFF/GAFF2 atom typing, tleap for building simulation systems, cpptraj for trajectory analysis, and reduce for hydrogen optimization.
Is AmberTools free to use?
Yes. AmberTools is distributed under the GPL-2.0 (Free) license and is available at no cost through the Paramus App Store.
How do I install AmberTools?
AmberTools 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 AmberTools for one-click deployment.
What are the key features of AmberTools?
Key features of AmberTools include: Parameterization: antechamber, parmchk2; System building: tleap, xleap; Analysis: cpptraj, pytraj; Force fields: GAFF, GAFF2, ff19SB.
What type of application is AmberTools?
AmberTools 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 AmberTools run on?
AmberTools 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 AmberTools be automated or integrated with AI workflows?
Yes. AmberTools 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 AmberTools in publications?
The recommended citation for AmberTools is: Case, D.A. et al. AmberTools. J. Chem. Inf. Model. 63, 6183-6191 (2023). DOI:10.1021/acs.jcim.3c01153