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PDB2PQR(1) PDB2PQR Manual PDB2PQR(1)

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
 
2008-06-04 pdb2pqr