AUTOGRID(1)

🎀 autogrid(1) 🎀

okay bestie, you've landed in the General Commands Manual and this is the page for autogrid, and honestly it's giving main character energy. hydrate, sit down, let's build you a grid 💖

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🌸 NAME 🌸

autogrid — preparing your protein and your ligand for AutoDock analysis. yeah, this is the pre-game. the vibe check before the docking. iykyk.

✨ SYNOPSIS ✨

autogrid4 [options] -p gridparameterfile

🦋 DESCRIPTION 🦋

so what is AutoGrid actually doing? it prepares a 3D grid representation of the non-covalent interaction energies that all your user-specified ligand atom types are gonna experience around a user-specified target macromolecule. that's the whole thing. that's the assignment. ✨

and it doesn't stop there — the electrostatic potential grid map and the desolvation free energy grid map can be calculated too, if you want them. obsessed.

the grid maps get stored in plain text files with the extension '.map', and AutoDock 4 literally needs them to perform dockings. no maps, no dockings, no cap.

AutoGrid also outputs:

• a '.xyz' file, which describes the spatial extents of the grid box 🌸
• an AVS field '.fld' file, which describes the consistent set of atomic affinity grid maps that were calculated together for a given target macromolecule 🦋

🚨 okay this part matters, listen up: it is necessary to compute grid maps for all the atom types in the ligand — or set of ligands — that will be docked, plus an electrostatic potential grid map and a desolvation free energy map. like, all of them. for example, if a ligand has an aliphatic carbon and a hydrogen-bond-accepting oxygen atom, it would be necessary to compute both a 'C' map and an 'OA' map. both bestie. two maps. don't be shy about it.

more info about AutoDock 4 atom types lives here:

http://autodock.scripps.edu/faqs-help/faq/where-do-i-set-the-autodock-4-force-field-parameters

and for prepping your input? the input to AutoGrid is best prepared with the program suite AutoDockTools. also — and i cannot stress this enough — there is no way to run autodock4 without a grid. periodt. 💅

💅 OPTIONS 💅

• -o — use old PDBq format (the q sits in columns 55-61)
• -u — usage information, also available as -h on Debian
• -d — increased verbosity of messages, for when you're deep in the debugging trenches helping yourself 🔍
• -l — logfile
• -p filename — specifies Grid Parameter File

🌈 EXAMPLE 🌈

a whole range of tests ships with the AutoGrid sources, and you can use them like this:

$ D=/usr/share/doc/autogrid/Tests
$ cd /tmp
$ ln -s $D/AD4_parameters.dat .
$ gunzip -c $D/hsg1_sm.pdbqt.gz > hsg1_sm.pdbqt
$ autogrid4 -p $D/hsg1_no_receptor_types.gpf -l hsg1_no_receptor_types.glg

this command prepares grid map files for each of the AutoDock atom types specified in the grid parameter file — in this case: hsg1_sm.A.map, hsg1_sm.C.map, hsg1_sm.d.map, hsg1_sm.e.map, hsg1_sm.HD.map, hsg1_sm.NA.map, hsg1_sm.N.map, hsg1_sm.OA.map — plus the AVS field file (hsg1_sm.maps.fld) and hsg1_sm.maps.xyz. eight maps and a whole little family of output files, ate that. 🔥

to perform the cocking calculation — yes bestie, the original page says "cocking", we don't make the rules, it means docking 🙈 — AutoDock should be executed, though it demands a separate docking parameter file (with extension .dpf). the DPF refers to the grid map files that are necessary to the docking, and it also lets you set other important parameters, like the search method and how many dockings to perform.

🫶 SEE ALSO 🫶

• autodock(1), runAdt(1)
• http://autodock.scripps.edu

📜 LICENSE 📜

this software is made available under the terms of the GNU Public License version 2 or later. which implies that this software may be redistributed if the source is made available. 🫶

but lowkey — it would help the future development of the AutoDockSuite if you register yourself at http://autodock.scripps.edu/downloads. do it for the girls. do it for science. do it for future you. ✨

👑 AUTHOR 👑

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

this manual page was written by Steffen Moeller <moeller@debian.org> and much revised by upstream author Garrett Morris. it was prepared for the Debian project but may be used by others, and is hopefully adopted by the upstream developers. fingers crossed, they deserve it. 🎀

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and that's the tea, bestie 💖 this was the AUTOGRID(1) page from the General Commands Manual, dated Juli 23, 2007 — go forth and compute every single atom type, you absolute icon 👑✨🌸