NAME

       pdb2pqr - Generate PQR files for use in electrostatics calculations

SYNOPSIS

       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}

DESCRIPTION

       pdb2pqr 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

OPTIONS

       pdb2pqr accepts the following options:

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

       --help, -h
           Print a help message and exit.

       --nodebump
           Do not perform debumping operation.

       --noopt
           Do not perform hydrogen optimization.

       --chain
           Keep the chain ID in the output PQR file.

       --assign-only
           Only assigns charges to add atoms, debump, or optimize.

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

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

       --with-ph=ph
           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.

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

       --ligand=path
           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

       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:

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

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

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

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

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

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

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

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

CITING PDB2PQR

       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).

SEE ALSO

       psize(1)

AUTHOR

       Manuel Prinz <debian@pinguinkiste.de>
           Wrote this manpage for the Debian System.

COPYRIGHT

       Copyright © 2008 Manuel Prinz