drug-mmpbsa-gbsa

What problem does it solve?

This Skill computes relative binding free-energy estimates for protein–ligand complexes directly from an already-generated protein–ligand MD trajectory, using the single-trajectory MM-GBSA / MM-PBSA end-point method.

Core Features & Use Cases

• Fast OpenMM GBn2 backend (MM-GBSA): rescoring via compute_mmgbsa.py with an OpenMM implicit solvent GBn2 model for high-throughput pose ranking.
• AmberTools MMPBSA backend (MM-GBSA and/or MM-PBSA): rescoring via compute_mmpbsa.py using MMPBSA.py to support both GB (multiple igb choices) and PB in one run.
• Trajectory-frame energy reporting: outputs per-frame energies and summary statistics, including caveats about correlated frames and the need for replicates.
• Practical drug-discovery use case: re-ranking HTVS-docked hits after MD refinement as an orthogonal signal to geometry/stability metrics.

Quick Start

Run a GB-only rescoring from your solvated complex topology and production DCD with the ligand SDF by executing python .agents/skills/drug-mmpbsa-gbsa/scripts/compute_mmgbsa.py --topology md/system/complex_solvated.pdb --trajectory md/run/production.dcd --ligand_sdf md/ligand.sdf --ligand_resname UNL --skip_ns 0.5 --stride 5 --output_dir md/mmgbsa/.