debian man page for pdb2pqr

Query: pdb2pqr

OS: debian

Section: 1

Format: Original Unix Latex Style Formatted with HTML and a Horizontal Scroll Bar

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: o Adding a limited number of missing heavy atoms to biomolecular structures o Determining side-chain pKas o Placing missing hydrogens o Optimizing the protein for favorable hydrogen bonding o 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 (C) 2008 Manuel Prinz pdb2pqr 2008-06-04 PDB2PQR(1)
Related Man Pages
g_chi(1) - debian
mkdssp(1) - debian
pdb2gmx(1) - debian
kpsewhich(1) - centos
kpsewhich(1) - osx
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