table of contents
| PROPKA3(1) | User Commands | PROPKA3(1) |
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:s}] (default: /build/propka-5Nidcz/propka-3.5.0/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)
| February 2023 | propka3 3.5.0 |