--- name: "pdb2pqr" section: "1" platform: "linux" package: "pdb2pqr" version: "3.6.1+dfsg-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/pdb2pqr30" --- # pdb2pqr(1) manual page for pdb2pqr30 3.6.1+dfsg Part of [pdb2pqr30(1)](/pdb2pqr30/1.md). ## 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 \, i.e. \ 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 \ and \ \[\.pir\] (default: None) - **-m** MUTATIONS, **--mutation** MUTATIONS specifying mutation labels which is used to modify \ 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 \ \[alignment/scwrl/jackal\] (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)