AUTODOCK(1)

✨ NAME ✨

okay so vina is the whole vibe here: it's docking small molecules against proteins. that's it, that's the gig — molecular matchmaking, no cap. 🧬💅

quick lil context bestie: this page lives in the General Commands Manual, and its official page name up top is AUTODOCK(1) — even though the program you actually type is vina. iykyk. 🎀

🌸 DESCRIPTION 🌸

here's the whole rundown, section by section, no skips, no skimming. every flag stays exactly where it was. 🫶

💌 Input 💌

the stuff you feed it going in:

• --receptor arg — the rigid part of the receptor (PDBQT). this is the solid, unmoving chunk of your protein.
• --flex arg — the flexible side chains, if there are any (PDBQT). so like, the wiggly bits. 💃
• --ligand arg — the ligand (PDBQT). the lil molecule you're docking. the main character, honestly. 👑

🔍 Search space (required) 🔍

this part is required, bestie — you cannot skip it. tell it where to look:

• --center_x arg — X coordinate of the center
• --center_y arg — Y coordinate of the center
• --center_z arg — Z coordinate of the center
• --size_x arg — size in the X dimension (Angstroms)
• --size_y arg — size in the Y dimension (Angstroms)
• --size_z arg — size in the Z dimension (Angstroms)

so that's a center point plus a box size, in three whole dimensions. slay. 📦✨

💾 Output (optional) 💾

not mandatory, but like… you probably want your results:

• --out arg — output models (PDBQT). the default is chosen based on the ligand file name. (it just picks for you, cute.)
• --log arg — optionally, write log file. receipts! 🧾

🛠️ Misc (optional) 🛠️

the little knobs and dials:

• --cpu arg — the number of CPUs to use. the default is to try to detect the number of CPUs or, failing that, use 1.
• --seed arg — explicit random seed. for when you need the randomness to be, like, not random. 🔮
• --exhaustiveness arg (=8) — exhaustiveness of the global search (roughly proportional to time): 1+. more = more searching = more time. periodt.
• --num_modes arg (=9) — maximum number of binding modes to generate
• --energy_range arg (=3) — maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)

📝 Configuration file (optional) 📝

• --config arg — the above options can be put here. yup, all of them. one file, everything tucked in. iconic. 🎀

ℹ️ Information (optional) ℹ️

• --help — display usage summary
• --help_advanced — display usage summary with advanced options (the deluxe version 💅)
• --version — display program version

👀 SEE ALSO 👀

• AutoDock Vina home page on http://vina.scripps.edu 🌐

okay that's the whole page, you made it to the end, proud of you fr fr. 🫶 this was AutoDock Vina 1.1.1 (Apr 20, ...), dated November 2010, and the page itself is filed under AUTODOCK(1). go dock something cute. 💖✨🦋