MM/GB(PB)SA

PaperCodeProduction Ready

Calculate protein-ligand or protein-protein binding free energy using Molecular mechanics/Generalized-Born (Poisson-Boltzmann) surface area

Readiness

Readiness: Production Ready
Smoke: passed
Artifacts: passed
Production: production_ready_cpu_unigbsa_1thread
Storage: <5
Strategy: shared python312_slim.sif + tool ext3 overlay
Next: Validate user-uploaded receptor/ligand files from the web UI and keep OMP_NUM_THREADS=1 unless larger benchmark confirms higher threading.

SOP validation used upstream Uni-GBSA revision 8eff7408f182db7778d615b58a27856c1eac8e88 at /media/nik/seagate_nik/bio_server/tools/mm-gb-pb-sa/source/Uni-GBSA with env /home/nik/micromamba-root/envs/mm-gb-pb-sa-py310. Worker Slurm job 343 completed with 1CEB BindingEnergy TOTAL -20.133892 kcal/mol. API Slurm job 345 / remote a2b915ea2377 completed in 15.107s with TOTAL -20.341796 kcal/mol and status S, close to upstream README value around -20.1781. Adapter sources amber.sh, uses OMP_NUM_THREADS=1 and -nt 1; conda env is under /home/nik because seagate_nik blocks symlink creation. Artifacts include BindingEnergy.csv, results.csv, summary.json, stdout/stderr, and Slurm logs.