---
name: "propka3"
section: "1"
platform: "linux"
package: "python3-propka"
version: "3.5.1-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/propka3"
---

# propka3(1)

predict pKa values of ionizable groups

## NAME

propka3 - predict pKa values of ionizable groups

## DESCRIPTION

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

PROPKA predicts the pKa values of ionizable groups in proteins and proteinligand complexes based in the 3D structure

### positional arguments:

- input\_pdb

  read data from \<filename\>

### options:

- **-h**, **--help**

  show this help message and exit

- **-f** FILENAMES, **--file** FILENAMES

  read data from \<filename\>, i.e. \<filename\> is added to arguments (default: \[\])

- **-r** REFERENCE, **--reference** REFERENCE

  setting which reference to use for stability calculations \[neutral/low-pH\] (default: neutral)

- **-c** CHAINS, **--chain** CHAINS

  creating the protein with only a specified chain. Specify " " for chains without ID \[all\] (default: None)

- **-i** TITRATE\_ONLY, **--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)

- **-t** THERMOPHILES, **--thermophile** THERMOPHILES

  defining a thermophile filename; usually used in 'alignment-mutations' (default: None)

- **-a** ALIGNMENT, **--alignment** ALIGNMENT

  alignment file connecting \<filename\> and \<thermophile\> \[\<thermophile\>.pir\] (default: None)

- **-m** MUTATIONS, **--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

- **-p** PARAMETERS, **--parameters** PARAMETERS

  set the parameter file (default: */build/reproduciblepath/propka-3.5.1/propka/propka.cfg*)

- **--log-level** {DEBUG,INFO,WARNING,ERROR,CRITICAL}

  logging level verbosity (default: INFO)

- **-o** PH, **--pH** PH

  setting pH-value used in e.g. stability calculations \[7.0\] (default: 7.0)

- **-w** WINDOW WINDOW WINDOW, **--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))

- **-g** GRID GRID GRID, **--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))

- **--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)

- **--protonate-all**

  Protonate all atoms (will not influence pKa calculation) (default: False)