AutoDock Vina Common Errors & Fixes (Online + Local)

Most “Vina is broken” posts are really prep or box problems. This checklist covers the failures that show up in coursework, BioStars, and local installs — and how to unblock with an online AutoDock Vina path when MGLTools or conda fights you.

1. “Parse error” / invalid PDBQT

• Cause: missing charges/atom types, truncated file, or receptor still has waters/altlocs that confuse the writer.
• Fix: regenerate PDBQT with a known engine (Open Babel or Meeko). Try free PDB to PDBQT online; clean waters first with PDB Cleaner.
• Online path: paste PDB ID + SMILES on Dock — Meeko writes PDBQT server-side, no ADT GUI.

2. MGLTools / AutoDockTools install crashes (Windows)

• Cause: old Python wheels, PATH conflicts, 32/64-bit mixes, antivirus locking DLLs.
• Fix: skip ADT for routine ligand prep. Use PDBQT converter or cloud Meeko. Keep local Vina binary only if your course requires CLI screenshots.

3. “No poses found” / empty output

• Cause: search box far from the pocket, box too small, wrong chain, or ligand MW/TORSDOF outside practical limits.
• Fix: redefine box from co-crystal ligand or residue anchors; preview in 3D. On Dock, Review setup (0 credits) catches many box/ligand issues before you spend Credits.
• Guide: prepare receptor & ligands.

4. Extremely similar scores for every analog

• Cause: oversized box (ligands float), identical wrong protonation, or scoring a decoy pocket.
• Fix: tighten to ~20 Å sides for drug-like ligands; redock the native ligand; compare PLIP, not third decimals. See what is a good Vina score.

5. High rotatable bonds / TORSDOF warnings

• Cause: peptides, long linkers, or poorly drawn SMILES with extra rotatable bonds.
• Fix: Dock warns above ~12 rotors and rejects above 20. Cap chemistry for coursework; note the limit in Methods.

6. “Ligand did not dock” on a cloud job

• Meaning: the pipeline ran but that molecule failed prep or scoring (bad SMILES, embedding failure, timeout) — not a platform outage.
• Fix: validate SMILES with name → SMILES or ChemDraw; remove salts; retry a smaller batch. Credits are not refunded for ligand-level failures (see FAQ on the homepage).

7. Redock RMSD looks terrible

• Cause: wrong ligand selected as reference, wrong chain, protonation mismatch, or box not centered on the co-crystal.
• Fix: confirm holo PDB and box source; read holo vs apo. Do not screen a library until redock is plausible.

8. Exhaustiveness / slow local runs on a laptop

• Cause: huge boxes, hundreds of flexible ligands, low RAM.
• Fix: shrink the box; batch fewer ligands; or run on Dock (fixed exhaustiveness 8 for reproducibility) and download ZIP/PDF for the report.

Quick decision tree

1. ADT/conda broken? → converter or Dock online.
2. Parse errors? → regenerate PDBQT; clean PDB.
3. Empty poses? → fix box + chain.
4. Scores meaningless? → redock + interactions, not magic cutoffs.

Next: step-by-step docking · thesis Methods paragraph · free prep tools.