pdb2pqr(1) Generate PQR files for use in electrostatics calculations


pdb2pqr [--nodebump] [--noopt] [--chain] [--assign-only] [--clean] [--ffout=name] [--with-ph=ph] [--apbs-input] [--ligand=path] [[--verbose] | [-v]] --ff=forcefield path output-path
pdb2pqr {--help | -h}



automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a utility for converting protein files in PDB format (path) to PQR format (output-path). These tasks include:

• Adding a limited number of missing heavy atoms to biomolecular structures

• Determining side-chain pKas

• Placing missing hydrogens

• Optimizing the protein for favorable hydrogen bonding

• Assigning charge and radius parameters from a variety of force fields


pdb2pqr accepts the following options:


The forcefield to use. Current values are amber, charm, parse and tyl06.

--help, -h

Print a help message and exit.


Do not perform debumping operation.


Do not perform hydrogen optimization.


Keep the chain ID in the output PQR file.


Only assigns charges to add atoms, debump, or optimize.


Do no optimization, atom addition, or parameter assignment, just return the original PDB file in alligned format.


Instead of using the standard caninical naming scheme for residue and atom names, use the names from the given forcefield.


Use propka to calculate pKas and apply them to the molecule given the pH value. Actual PropKa results will be output to output-path.propka.


Create an APBS input file based on the generated PQR file. Also create a Python pickle for using these parameters in other programs.


Calculate the parameters for the ligand in MOL2 format at the given path. Pdb2pka must be compiled.

--verbose, -v

Print additional information to screen.


Extensions add functionality to PDB2PQR and are called by passing a parameter to pdb2pqr. They put their results into files located in output-path.

The following extensions can be used by pdb2pqr:


Print the per-residue backbone phi angle to output-path.phi.


Print the per-residue backbone psi angle to output-path.phi.


Print a list of hygrogen bonds to output-path.hbond.


Print the per-residue backbone chi angle to output-path.chi.


Print a list of contacts to output-path.con.


Print a list of hydrogen bonds to output-path.hbo.


Print a list of salt bridges to output-path.salt.


Print the per-residue phi and psi angles to outpath-path.rama.


Please acknowledge your use of pdb2pqr by citing:

Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research, 32, W665-W667 (2004).


Manuel Prinz <[email protected]>

Wrote this manpage for the Debian System.


Copyright © 2008 Manuel Prinz