3. propka3 command¶

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure. The propka3 command has the following options:

propka3 [-h] [-f FILENAMES] [-r REFERENCE] [-c CHAINS] [-i TITRATE_ONLY] [-t THERMOPHILES] [-a ALIGNMENT] [-m MUTATIONS]
       [-v VERSION_LABEL] [-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] [--generate-propka-input]
       [--protonate-all]
       input_pdb

input_pdb¶: read data from file <input_pdb>

-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)

-v VERSION_LABEL, --version VERSION_LABEL¶: specifying the sub-version of propka [Jan15/Dec19] (default: Jan15)

-p PARAMETERS, --parameters PARAMETERS¶: set the parameter file (default: <installation_directory>/propka/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 (default: 7.0)

-w WINDOW WINDOW WINDOW, --window WINDOW WINDOW WINDOW¶: setting the pH-window to show e.g. stability profiles (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 (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)

--generate-propka-input¶: Generate a PROPKA input file (default: False)

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