propka3 - predict pKa values of ionizable groups
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
- -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)