g_mmpbsa

PaperCodeProduction Ready

Estimate binding free energy (ΔGbind) from protein-ligand or protein-protein trajectories.

Readiness

Readiness: Production Ready
Smoke: passed
Artifacts: passed
Production: ready
Storage: <5
Strategy: shared python312_slim.sif + g_mmpbsa_py312_site + upstream g_mmpbsa average/decompose post-processing fixtures
Next: Production Ready for scoped g_mmpbsa average/decompose post-processing mode. Full APBS/GROMACS trajectory mode remains future container work.

No obvious large model/database dependency identified; validate upstream docs before install. 2026-07-05 SOP batch recheck: backend inventory found no staged g_mmpbsa binary/source/fixture/artifacts/runner. Upstream precompiled g_mmpbsa can be standalone and this is a CPU MD post-processing tool, not a GPU tool; no direct Slurm MM-PBSA smoke has run. Kept Smoke Pending with GPU flag corrected to no. 2026-07-05 18:21 +08:00 backend re-audit: no staged g_mmpbsa binary/source/fixture/SIF/artifacts/runner found; GPU requirement remains corrected to no, but no MM-PBSA smoke evidence exists. Kept Smoke Pending. 2026-07-06 17:05 +08:00 direct Slurm smoke passed for scoped g_mmpbsa post-processing mode. Job 464, run /media/nik/seagate_nik/bio_server/runs/g-mmpbsa/smoke_20260706_170500, source rev 2fd8c9d0f23843224c02cc05b8c135409119cd16. Used official average/decompose calculations on bundled reference MM/PBSA component outputs and generated summary_energy.dat/csv, full_energy.dat, final_contrib_energy.dat/csv, energyMapIn.dat, results.csv, summary.json, and logs. Sanity: binding_average_kj_mol=-210.694, binding_error_kj_mol=19.741, residue contribution rows=199, total energy range -120.407 to 22.5287. Caveat: full g_mmpbsa trajectory/tpr/APBS/GROMACS run mode remains blocked until an APBS/GROMACS-backed build is available; upstream optional average CSV formatter raises AttributeError(list.length), so SOP CSVs are derived from official text outputs. 2026-07-08T00:21:35+08:00 SOP runner-adapter pass: added real backend adapter using shared python312_slim.sif and g_mmpbsa_py312_site. Ubuntu runner API job 3533b9527921 / Slurm job 522 passed official average/decompose post-processing with binding_average_kj_mol=-210.694, binding_error_kj_mol=19.741, 199 residue contribution rows, summary_energy/full_energy/final_contrib/energyMap artifacts, job.log, slurm.out, and zero-byte slurm.err.