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]
       [-v VERSION_LABEL] [-p PARAMETERS] [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-o PH] [-w WINDOW WINDOW WINDOW]
       [-g GRID GRID GRID] [-d] [-l] [-k] [-q] [--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)

--version

show program’s version number and exit

-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))

-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)