PDB2PQR30

NAME

pdb2pqr30 - manual page for pdb2pqr30 3.5.2+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 v3.5.2: 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)