autodock-vina
Structure-based docking with AutoDock Vina, Vinardo, and AutoDock4 through the Meeko toolchain. Use this skill to define a docking box, prepare receptors and ligands as PDBQT, run single or batch docking, rescore, and interpret affinities, poses, and ligand efficiency. Covers box definition from a reference ligand or pocket residues, protonation and tautomer decisions, flexible side chains, exhaustiveness and seeds, redocking validation, and virtual screening over compound libraries. Also trigger on vina, smina, gnina, mk_prepare_ligand, mk_prepare_receptor, mk_export, scrub.py, PDBQT, autogrid4, docking box, or binding-pose prediction.
- Version
- 1.0
- License
- MIT
- Compatibility
- The bundled scripts need only Python 3.10+ and the standard library. Running a docking calculation additionally needs the AutoDock Vina binary (conda install -c conda-forge vina, or pip install vina 1.2.7) and Meeko 0.7+ (pip install meeko) on PATH; SMILES input also needs molscrub. CPU only; no GPU or API key required.
Pinned to revision f67572246d9b, so it is the text this page describes rather than whatever the author pushed since.
Pre-approved tools experimental
Experimental field. Support varies between clients, so this list is what the author declared, not what your client will enforce.
- Read
- Write
- Edit
- Bash
Files
- skills/autodock-vina/SKILL.md
- skills/autodock-vina/references/ligand-preparation.md
- skills/autodock-vina/references/receptor-preparation.md
- skills/autodock-vina/references/scoring-and-interpretation.md
- skills/autodock-vina/references/troubleshooting.md
- skills/autodock-vina/scripts/dock_batch.py
- skills/autodock-vina/scripts/make_box.py
- skills/autodock-vina/scripts/parse_vina_output.py
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