PROPKA 3.1 Tutorial and user guid are not reachable.

[MaryamQ6]

Hi ,
I was trying to compute pKa using PROPKA source after closing the server,
but when calculating there was no tutorial or user guide were reachable to get to know how to use argument to change force filed and other options was availale on the server.

any idea where to get program documentation? Or auther contact

best,
maryam

[mgarort]

Did anyone find the tutorial? Would be greatly appreciated.

Thanks.

[orbeckst]

Try

propka31 --help

which gives the basics

propka31 -h
usage: propka31 [-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

PROPKA predicts the pKa values of ionizable groups in proteins and protein-
ligand complexes based in the 3D structure

positional arguments:
  input_pdb             read data from <filename>

optional arguments:
  -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:s}] (default: ~/miniconda2/envs/propka/lib/python3
                        .6/site-packages/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)
  --generate-propka-input
                        Generate a PROPKA input file (default: False)
  --protonate-all       Protonate all atoms (will not influence pKa
                        calculation) (default: False)

Docs and tutorials are missing. Contributions are welcome!

[orbeckst]

Duplicate of #27

[orbeckst]

Closed with #27