Provided by: pdb2pqr_3.6.1+dfsg-1_all bug

NAME

       pdb2pqr30 - manual page for pdb2pqr30 3.6.1+dfsg

DESCRIPTION

       usage: pdb2pqr [-h] [--ff {AMBER,CHARMM,PARSE,TYL06,PEOEPB,SWANSON}]

              [--userff  USERFF]  [--clean] [--nodebump] [--noopt] [--keep-chain] [--assign-only]
              [--ffout   {AMBER,CHARMM,PARSE,TYL06,PEOEPB,SWANSON}]    [--usernames    USERNAMES]
              [--apbs-input    APBS_INPUT]    [--pdb-output    PDB_OUTPUT]    [--ligand   LIGAND]
              [--whitespace]   [--neutraln]   [--neutralc]   [--drop-water]    [--include-header]
              [--titration-state-method  {propka}]  [--with-ph  PH] [-f FILENAMES] [-r REFERENCE]
              [-c CHAINS] [-i TITRATE_ONLY] [-t THERMOPHILES] [-a ALIGNMENT] [-m  MUTATIONS]  [-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]  [--version] input_path
              output_pqr

       PDB2PQR v3.6.1: biomolecular structure conversion software.

   positional arguments:
       input_path
              Input PDB path or ID (to be retrieved from RCSB database

       output_pqr
              Output PQR path

   options:
       -h, --help
              show this help message and exit

       --version
              show program's version number and exit

   Mandatory options:
              One of the following options must be used

       --ff {AMBER,CHARMM,PARSE,TYL06,PEOEPB,SWANSON}
              The forcefield to use. (default: PARSE)

       --userff USERFF
              The user-created forcefield file to use. Requires --usernames  and  overrides  --ff
              (default: None)

       --clean
              Do  no  optimization,  atom  addition,  or  parameter  assignment,  just return the
              original PDB file in aligned format. Overrides --ff and --userff (default: False)

   General options:
       --nodebump
              Do not perform the debumping operation (default: True)

       --noopt
              Do not perform hydrogen optimization (default: True)

       --keep-chain
              Keep the chain ID in the output PQR file (default: False)

       --assign-only
              Only assign charges and radii - do not add atoms, debump,  or  optimize.  (default:
              False)

       --ffout {AMBER,CHARMM,PARSE,TYL06,PEOEPB,SWANSON}
              Instead  of  using the standard canonical naming scheme for residue and atom names,
              use the names from the given forcefield (default: None)

       --usernames USERNAMES
              The user-created names file to use. Required if using --userff (default: None)

       --apbs-input APBS_INPUT
              Create a template APBS input file based on the generated PQR file at the  specified
              location.  (default: None)

       --pdb-output PDB_OUTPUT
              Create  a PDB file based on input. This will be missing charges and radii (default:
              None)

       --ligand LIGAND
              Calculate the parameters for a single MOL2-format ligand at the path  specified  by
              this  option.  The  MOL2  ligand name should match only one ligand in the PDB file.
              (default: None)

       --whitespace
              Insert whitespaces between atom name and residue name, between x and y, and between
              y and z. (default: False)

       --neutraln
              Make the N-terminus of a protein neutral (default is charged). Requires PARSE force
              field. (default: False)

       --neutralc
              Make the C-terminus of a protein neutral (default is charged). Requires PARSE force
              field. (default: False)

       --drop-water
              Drop waters before processing biomolecule. (default: False)

       --include-header
              Include  pdb header in pqr file. WARNING: The resulting PQR file will not work with
              APBS versions prior to 1.5 (default: False)

   pKa options:
              Options for titration calculations

       --titration-state-method {propka}
              Method used to calculate titration states. If a titration state method is selected,
              titratable  residue charge states will be set by the pH value supplied by --with_ph
              (default: None)

       --with-ph PH
              pH values to use when applying the results of the selected pH  calculation  method.
              (default: 7.0)

   PROPKA invocation options:
       -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)

       -p PARAMETERS, --parameters PARAMETERS
              set         the         parameter        file        [{default:s}]        (default:
              /usr/lib/python3/dist-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)

       --protonate-all
              Protonate all atoms (will not influence pKa calculation) (default: False)