Command Line Usage

The command line version of PDB2PQR must be installed from source using the instructions in the PDB2PQR download section of the Accessing the Software section. This version of the software offers an expanded range of options and can also be customized with user extensions.

The command line PDB2PQR is invoked as

% $ python pdb2pqr.py [options] --ff={forcefield} {path} {output-path}

This module takes a PDB file as input and performs optimizations before yielding a new PQR-style file in {output-path}. If {path} is an ID it will automatically be obtained from the PDB archive.

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Options
--version</td>show program's version number and exit
-h, --helpshow this help message and exit
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Mandatory Options
One of the options must be used.
--ff=FIELD_NAME</td> The forcefield to use - currently amber, charmm, parse, tyl06, peoepb and swanson are supported.
--userff=USER_FIELD_FILEThe user created forcefield file to use. Requires --usernames overrides --ff
--cleanDo no optimization, atom addition, or parameter assignment, just return the original PDB file in aligned format. Overrides --ff and --userff
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General Options
--nodebumpDo not perform the debumping operation
--nooptsDo not perform hydrogen optimization
--chainKeep the chain ID in the output PQR file
--assign-onlyOnly assign charges and radii - do not add atoms, debump, or optimize.
--ffout=FIELD_NAMEInstead of using the standard canonical naming scheme for residue and atom names, use the names from the given forcefield - currently amber, charmm, parse, tyl06, peoepb and swanson are supported.
--usernames=USER_NAME_FILEThe user created names file to use. Required if using --userff
--apbs-inputCreate a template APBS input file based on the generated PQR file. Also create a Python pickle for using these parameters in other programs.
--ligand=PATHCalculate the parameters for the ligand in mol2 format at the given path. Pdb2pka must be compiled.
--whitespaceInsert whitespaces between atom name and residue name, between x and y, and between y and z.
--typemap</td>Create Typemap output.
--neutralnMake the N-terminus of this protein neutral (default is charged). Requires PARSE force field.
--neutralcMake the C-terminus of this protein neutral (default is charged). Requires PARSE force field.
-v, --verbose</nobr>Print information to stdout.
--drop-water</nobr>Drop waters before processing protein. Currently recognized and deleted are the following water types:HOH, WAT
--include_headerInclude pdb header in pqr file. WARNING: The resulting PQR file will not with APBS versions prior to 1.5
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pH options
--ph-calc-method=PH_METHOD</td>Method used to calculate ph values. If a pH calculation method is selected, for each titratable residue pH values will be calculated and the residue potentially modified after comparison with the pH value supplied by --with_ph
PROPKA - Use PROPKA to calculate pH values. Actual PROPKA results will be output to .propka.
PDB2PKA - Use PDB2PKA to calculate pH values. Requires the use of the PARSE force field. Warning: Larger residues can take a very long time to run using this method. EXPERIMENTAL!</td></tr>
--with-ph=PHpH values to use when applying the results of the selected pH calculation method. Defaults to 7.0
PDB2PKA options
--pdb2pka-out=PDB2PKA_OUTOutput directory for PDB2PKA results. Defaults to pdb2pka_output.
--pdb2pka-resumeResume run from state saved in output directory.
--pdie=PDB2PKA_PDIEProtein dielectric constant. Defaults to 8
--sdie=PDB2PKA_SDIESolvent dielectric constant. Defaults to 80
--pairene=PDB2PKA_PAIRENECutoff energy in kT for calculating non charged-charged interaction energies. Default: 1.0
proPKA options
--propka-reference=PROPKA_REFERENCESetting which reference to use for stability calculations. See PROPKA 3.0 documentation.
--propka-verbosePrint extra proPKA information to stdout. WARNING: This produces an incredible amount of output.
Extension options
--chiPrint the per-residue backbone chi angle to {output-path}.chi
--summaryPrint protein summary information to {output-path}.summary.
--contactPrint a list of contacts to {output-path}.con
--newresinterPrint interaction energy between each residue pair in the protein to {output-path}.newresinter.
--saltPrint a list of salt bridges to {output-path}.salt
Hbond extension options
--hbondPrint a list of hydrogen bonds to {output-path}.hbond
--whatifChange hbond output to WHAT-IF format.
--angle_cutoff=ANGLE_CUTOFFAngle cutoff to use when creating hbond data (default 30.0)
--distance_cutoff=DISTANCE_CUTOFFDistance cutoff to use when creating hbond data (default 3.4)
--old_distance_methodUse distance from donor hydrogen to acceptor to calculate distance used with --distance_cutoff.
Resinter extension options
--resinterPrint interaction energy between each residue pair in the protein to {output-path}.resinter.
--residue_combinationsRemap residues to different titration states and rerun resinter appending output. Consider only the minimum number of whole protein titration combinations needed to test each possible pairing of residue titration states. Normally used with --noopt. If a protein titration state combination results in a pair of residue being re-tested in the same individual titration states a warning will be generated if the re-tested result is different. This warning should not be possible if used with --noopt.
--all_residue_combinationsRemap residues to ALL possible titration state combinations and rerun resinter appending output. Results with --noopt should be the same as --residue_combinations. Runs considerably slower than --residue_combinations and generates the same type of warnings. Use without --noopt to discover how hydrogen optimization affects residue interaction energies via the warnings in the output.
Rama extenstion options
--ramaPrint the per-residue phi and psi angles to {output-path}.rama for Ramachandran plots
--phi_onlyOnly include phi angles in output. Rename output file {output-path}.phi</nobr>
--psi_onlyOnly include psi angles in output. Rename output file {output-path}.psi