PROPKA3(1)

💖 propka3 — the pKa-predicting bestie 💖

okay so. you know how proteins are lowkey just little blobs of vibes that fall apart when the pH gets weird? yeah. propka3 from the PROPKA3(1) manual (User Commands section, iykyk) is the girl who tells you exactly when each ionizable group is gonna flip its proton off. she's that friend. she's the main character. 🫶

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✨ NAME ✨

propka3 — predict pKa values of ionizable groups

like. that's her whole job. that's the assignment and she ate. 💅

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🌸 DESCRIPTION 🌸

here's the whole ~vibe~, the usage line, verbatim, no cap:

usage: propka3 [-h] [-f FILENAMES] [-r REFERENCE] [-c CHAINS]
       [-i TITRATE_ONLY] [-t THERMOPHILES] [-a ALIGNMENT] [-m MUTATIONS]
       [--version] [-p PARAMETERS] [--log-level
       {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-o PH] [-w WINDOW WINDOW WINDOW]
       [-g GRID GRID GRID] [--mutator MUTATOR] [--mutator-option
       MUTATOR_OPTIONS] [-d] [-l] [-k] [-q] [--protonate-all] input_pdb

so the actual tea: PROPKA predicts the pKa values of ionizable groups in proteins and proteinligand complexes based in the 3D structure. 🧚 that's it. that's the whole plot. you hand her a structure, she hands you back the pKa receipts.

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🎀 positional arguments 🎀

• input_pdb — read data from <filename>. yes bestie, this one's required, you gotta feed her something. 🍓

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👑 OPTIONS 👑

one bullet per flag, no skipping, no summarising, we're doing the FULL list. buckle up. 🌈

• -h, --help — show this help message and exit. the classic. the goat. 🫶
• -f, --file FILENAMES — read data from <filename>, i.e. <filename> is added to arguments (default: [])
• -r, --reference REFERENCE — setting which reference to use for stability calculations [neutral/low-pH] (default: neutral)
• -c, --chain CHAINS — creating the protein with only a specified chain. Specify " " for chains without ID [all] (default: None)
• -i, --titrate_only TITRATE_ONLY — Treat only the specified residues as titratable. Value should be a comma-separated list of "chain:resnum" values; for example: -i "A:10,A:11" (default: None). so like, pick your favs and ignore everyone else. iconic behaviour honestly.
• -t, --thermophile THERMOPHILES — defining a thermophile filename; usually used in 'alignment-mutations' (default: None)
• -a, --alignment ALIGNMENT — alignment file connecting <filename> and <thermophile> [<thermophile>.pir] (default: None)
• -m, --mutation MUTATIONS — specifying mutation labels which is used to modify <filename> according to, e.g. N25R/N181D (default: None)
• --version — show program's version number and exit. the little "who am i" moment. ⭐
• -p, --parameters PARAMETERS — set the parameter file (default: /build/propkavqnmhG/propka-3.5.1/propka/propka.cfg)
• --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL} — logging level verbosity (default: INFO). turn it up to DEBUG when you want her to overshare. 😭
• -o, --pH PH — setting pH-value used in e.g. stability calculations [7.0] (default: 7.0)
• -w, --window WINDOW WINDOW WINDOW — setting the pH-window to show e.g. stability profiles [0.0, 14.0, 1.0] (default: (0.0, 14.0, 1.0)). notice how this one takes THREE values. she's extra like that. 💅
• -g, --grid GRID GRID GRID — setting the pH-grid to calculate e.g. stability related properties [0.0, 14.0, 0.1] (default: (0.0, 14.0, 0.1)). also three values. yes bestie, three.
• --mutator MUTATOR — setting approach for mutating <filename> [alignment/scwrl/jackal] (default: None)
• --mutator-option MUTATOR_OPTIONS — setting property for mutator [e.g. type="side-chain"] (default: None)
• -d, --display-coupled-residues — Displays alternative pKa values due to coupling of titratable groups (default: False)
• -l, --reuse-ligand-mol2-files — Reuses the ligand mol2 files allowing the user to alter ligand bond orders (default: False)
• -k, --keep-protons — Keep protons in input file (default: False)
• -q, --quiet — suppress non-warning messages (default: None). she goes silent but she's still watching. 🙈
• --protonate-all — Protonate all atoms (will not influence pKa calculation) (default: False)

⚠️ quick heads-up for the -i, --titrate_only girlies: the value is a comma-separated list of "chain:resnum" values, like -i "A:10,A:11". don't freehand it and then act surprised. 💀

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🌟 SEE ALSO 🌟

ngl bestie, the original page didn't hand us any SEE ALSO links, so this is just me, wishing you luck, and reminding you to read the --help output. 😌

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that's the whole page, literally all of it, nothing dropped, nothing invented. propka3 3.5.1, dated January 2026, and this was the PROPKA3(1) page — take care of her, she's doing her best. 💖 ✨ 🦋