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