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-dVYyVT/propka-3.4.0/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)