MM/PBSA binding free-energy estimates from MD trajectories
Rank related ligands with an end-state free-energy estimate. ReactorMD selects stable trajectory frames, calculates MM/PBSA or MM/GBSA energies, decomposes the contributions by residue and reports the uncertainty.
Who this service is for
- Researchers comparing several ligands on one target
- Students adding free-energy support to MD results
- Groups needing per-residue energy contributions
What to send us
- Production trajectories for each complex and matching topologies
- The stable time window or permission to select it
- Receptor and ligand group definitions
How the work is done
- Verify the trajectory is equilibrated and select a stable window.
- Extract frames at a defined interval.
- Compute MM/PBSA or MM/GBSA binding energies.
- Decompose the energy per residue.
- Report averages with standard deviation and error estimates.
What you receive
- Binding energy table with components (van der Waals, electrostatic, polar and non-polar solvation)
- Per-residue decomposition plot
- Frame selection and settings
- Interpretation and limitations
What this method can and cannot tell you
MM/PBSA is an approximate method. It ranks similar ligands better than it predicts absolute affinity, and results vary with frame selection and dielectric settings.
Frequently asked questions
What is MM/PBSA?
Molecular Mechanics Poisson–Boltzmann Surface Area is an end-state method that estimates binding free energy from snapshots of an MD simulation.
Is MM/PBSA the same as experimental affinity?
No. It gives relative estimates that are most reliable for comparing related ligands on the same target.
What is the difference between MM/PBSA and MM/GBSA?
They differ in how solvation is treated. GB is faster, PB is more rigorous but slower.
Do I need to run the MD with ReactorMD?
No. Existing trajectories are accepted if they are well equilibrated.
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Computational results are predictions and support, but do not replace, experimental validation. Page reviewed by ReactorMD, 16 October 2026.