AUTODOCK(1)

✨ AUTODOCK ✨ — autodock(1), from the General Commands Manual, bestie 💖

okay so. picture this: you've got a tiny molecule and a big ol' protein and you NEED to know how they're gonna cuddle up together. that's this. that's the whole vibe. welcome to autodock 🧚

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🌸 NAME 🌸

autodock — docking of chemical ligands to protein receptors. no cap, that's the entire job description 💅

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🎀 SYNOPSIS 🎀

autodock4 [options]

that's it. that's the summoning ritual ✨

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🦋 DESCRIPTION 🦋

okay so AutoDock performs the automated docking of chemical compounds to proteins — i.e. it predicts how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. it's giving matchmaker but for molecules 💖

the AutoDockSuite consists of two main programs, and like… they're a duo, a dynamic duo, a main character and her right hand:

• AutoDock performs the docking of the ligand to a set of grids describing the target protein 🫶
• AutoGrid pre-calculates these grids ✨

one docks, one preps. iconic division of labour, honestly 👑

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💅 OPTIONS 💅

• -p parameter_filename — you hand it the parameter file, it does the thing 🌸
• -l log_filename — where the log goes 📓
• -o — Use old PDBQ format, charge q in columns 55-61. retro!! vintage!! the way it's literally numbered columns 😭
• -k — Keep original residue numbers. don't renumber my girls 🙈
• -i — Ignore header-checking. living dangerously, love that for you 💀
• -t — Parse the PDBQ file to check torsions, then stop. it's a vibe check and then it LEAVES 🚪
• -c < command_file — Command mode, by file
• -c | control_program — Command mode, by control_program

not me writing the < and | exactly as they appear bc the manpage says so and we do NOT improvise around here 💖

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🌈 EXAMPLE 🌈

on Debian, the directory /usr/share/doc/autodock offers examples to run. change to that directory and unpack (as root) the gzipped map files, then execute AutoDock as shown below:

gunzip *.map.gz
autodock4 -p 1pgp.dpf -l /tmp/1pgp.dlg

and boom, you're docking ✨ (as root though, so like, be normal about it 🫶)

the interpretation of results is aided by the AutoDockTools suite. please also inspect the tutorials offered online — fr fr, go read them, they ate 👑

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⭐ SEE ALSO ⭐

• autogrid(1), runAdt(1)
• http://autodock.scripps.edu
• http://autodock.scripps.edu/faqs-help/faq/what-is-the-command-line-to-start-autodock-4

(the second link got line-broken in the original at command-line-to- / start-autodock-4, so if you copy it, mind the join 😭)

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📜 LICENSE 📜

this software is made available under the terms of the GNU Public License version 2 or later. this implies that this software may be redistributed if the source is made available. it would however help the future development of the AutoDockSuite if you register yourself at http://autodock.scripps.edu/downloads 🫶

like, legally you're fine, but emotionally? go register. it's the nice thing to do 💖

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👑 AUTHOR 👑

the most prominent author of the version 4 of autodock is G. Morris <garrett@scripps.edu>. see the AUTHORS file in /usr/share/doc/autodock for details 📖

this manual page was written by Steffen Moeller <moeller@debian.org>, for the Debian project (but may be used by others and is hopefully adopted by the upstream developers) 🌸

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and that's the whole page, bestie!! this one's from the General Commands Manual, dated Juli 23, 2007 — yes, Juli, German spelling, we love a multilingual moment 🇩🇪 — and it's the AUTODOCK(1) page. now go dock something 💅✨🦋