pdb2pqr - 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}
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
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 aligned 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 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.
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 <debian@pinguinkiste.de>
Wrote this manpage for the Debian System.
Copyright © 2008 Manuel Prinz