Simulation · Amber consortium
AmberTools
A molecular simulation suite providing parameterisation, solvation, and free-energy evaluation for molecular systems.
What AmberTools is
AmberTools is a simulation package developed by the Amber consortium, incorporating the Amber force field family alongside an extensive toolchain for molecular dynamics and free-energy workflows. It is used to prepare, parameterise, and evaluate molecular models across structural biology and computational chemistry.
The software addresses critical steps in simulation preparation and post-docking evaluation. It supplies routines for molecular parameterisation, system solvation, and binding free-energy estimations using MM/PBSA and MM/GBSA methods to evaluate protein structures and small molecules.
Key facts
- Version
- 24
- Domain
- Simulation
- Tasks
- Molecular dynamics, free energy
- Modalities
- Protein structure, small molecule
- GPU memory
- 40 GB
What you can use it for
- Post-docking free energy calculation
- Running MM/PBSA and MM/GBSA analyses downstream of molecular docking to estimate binding energetics.
- System parameterisation and solvation
- Preparing protein and small-molecule structures by assigning force field parameters and building solvent environments.
- Structural and energetic analysis
- Generating tabular structural and thermodynamic summary data to assess molecular dynamics trajectories.
Run it here
No installation and no GPU of your own: fill in the inputs and it runs on our servers. Results stay in your browser unless you sign in.
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AmberTools
Strengths and limits
Good at
- Integrates the Amber force field family with a complete toolchain for simulation preparation and analysis.
- Provides established downstream docking workflows including MM/PBSA and MM/GBSA free-energy calculations.
- Acts as an integrated preparation and analysis layer for molecular dynamics engines.
Watch out for
- Requires 40 GB of GPU memory.
- Requires structure inputs to be supplied in PDB format.
Inputs and outputs
You provide
Structure (PDB)
You get back
Energetic and structural analysis.
Licence
Check the licence before commercial use · GPL-3.0
The GPL-3.0 licence carries terms worth reading before you depend on it.
Questions
Can I use AmberTools commercially?
Check the licence before commercial use. The GPL-3.0 licence carries terms worth reading before you depend on it.
How do I run AmberTools without installing anything?
Use the form under “Run it here” on this page: fill in the inputs and press Run model. It runs on our servers on 4–8× A100/H100, typically in 2.0h, and a run costs about 21,000 credits. Visitors without an account get 1,000 credits a month.
What tasks does AmberTools perform?
AmberTools performs molecular dynamics preparation, solvation, parameterisation, and free-energy calculations such as MM/PBSA and MM/GBSA.
What input formats are supported?
AmberTools takes structural inputs in PDB format.
What outputs are generated by the analysis pipeline?
The pipeline outputs tabular data detailing energetic and structural analyses.
Written from AmberTools's own documentation. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.