Docking & Binding · Amber consortium
MM/GBSA
Estimates binding free energies to rank congeneric small-molecule series against protein targets.
What MM/GBSA is
MM/GBSA is an end-point free energy tool developed by the Amber consortium and released in AmberTools 24. Designed for molecular docking workflows involving protein structures and small molecules, it calculates binding free energies across simulation frames.
The method trades the rigorous sampling of free energy perturbation for computational tractability, offering a faster alternative when screening compounds. Although it does not produce dependable absolute binding free energies, it reliably ranks congeneric series to inform compound selection for synthesis.
Key facts
- Version
- AmberTools 24
- Domain
- docking
- Task
- free_energy
- GPU memory
- 16 GB
What you can use it for
- Ranking congeneric series
- Ranks closely related chemical analogues to guide decisions for subsequent rounds of chemical synthesis.
- Tractable free energy estimation
- Serves as an end-point free energy alternative that runs faster than alchemical free energy perturbation.
- Per-residue energy decomposition
- Breaks down total binding free energy into individual residue contributions across molecular trajectory frames.
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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MM/GBSA
Strengths and limits
Good at
- Runs faster than alchemical free energy perturbation methods.
- Effectively ranks close analogues within a congeneric series.
- Provides per-residue free energy component breakdowns alongside the total free energy.
Watch out for
- Does not produce reliable absolute binding free energies.
- Requires 16 GB of GPU memory.
Inputs and outputs
You provide
Complex (PDB)
Trajectory framesoptional
You get back
ΔG components per residue and total.
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 MM/GBSA 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 MM/GBSA 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 2× A100, typically in 10min, and a run costs about 2,800 credits. Visitors without an account get 1,000 credits a month.
Can this method compute reliable absolute binding free energies?
No. The method is designed to trade rigour for speed and cannot be relied upon for accurate absolute binding free energies, though it remains useful for relative ranking.
What inputs does the method require?
It requires the coordinate structure of the complex in PDB format and the number of trajectory frames to evaluate.
What information is included in the output?
The output is a tabular summary of binding free energy components calculated per residue alongside the total free energy.
Written from MM/GBSA's own documentation. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.