aminak

Exact Vina invocation used for Task A

All 50 docks (10 conditions x 5 seeds) used identical box / scoring parameters. The literal CLI for one example — R215A_N226A_holo, seed 42 — is:

/opt/homebrew/bin/vina \
  --receptor /Users/ario/conserved_site_project/07e_mut_docking_v5/R215A_N226A/R215A_N226A_holo.pdbqt \
  --ligand   /Users/ario/conserved_site_project/05b_ligand_v2/dump.pdbqt \
  --center_x -0.137 --center_y 4.232 --center_z 15.159 \
  --size_x   18.0   --size_y   18.0  --size_z   18.0 \
  --exhaustiveness 32 \
  --num_modes      20 \
  --seed           42 \
  --out /Users/ario/conserved_site_project/12_phase7/01_replicas/raw/R215A_N226A_holo_seed42.pdbqt

Box parameters

Parameter Value
Centroid x -0.137
Centroid y 4.232
Centroid z 15.159
Box size x/y/z 18.0 A x 18.0 A x 18.0 A
Exhaustiveness 32
num_modes 20
Seeds 42, 7, 13, 99, 256
CPU 4 (auto)
Receptor format PDB2PQR-corrected -> Meeko PDBQT
Ligand dUMP, 5 active torsions (heavy=20)

The centroid is the chain-A active-site Cα centroid carried over from the v3/v4/v5 canonical pipeline (the v5 mutant runs that produced 07e_mut_docking_v5/mutant_results_v5.csv). The 18-A cubic box is slightly smaller than the v5 22-A canonical box; this is intentional — Phase 7 is specifically asking for stochastic noise floor of a tight box around the dUMP pocket, not a wide rescore.

Reproducing one run from scratch

  1. Source the environment: source 00_setup/env.sh.
  2. Confirm the receptor and ligand PDBQTs exist (paths above).
  3. Run the CLI exactly as shown, keeping --out so the docked poses are captured. The --seed flag fully determines the run, so identical commands are bit-reproducible on the same Vina build.
  4. Parse the top affinity from stdout (line starting with ` 1` after the dashed table header).
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