table of contents
PDB2PQR(1) | PDB2PQR Manual | PDB2PQR(1) |
NAME¶
pdb2pqr - Generate PQR files for use in electrostatics calculationsSYNOPSIS¶
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¶
•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=forcefieldThe 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: --phiPrint 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 Prinz2008-06-04 | pdb2pqr |