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
- • 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).
COPYRIGHT
Copyright © 2008 Manuel Prinz