apbs(1) [debian man page]

APBS(1) 							   User Commands							   APBS(1)

NAME

       abps - Adaptive Poisson Boltzmann Solver

SYNOPSIS

       apbs [options] parameters-file

DESCRIPTION

       The apbs command calculates electrostatic potentials, energies, and forces using both multigrid and finite element methods.

OPTIONS

       At the moment, the following options are supported:

       --output-file=<name>
	      Enables output logging to the path listed in <name>.  Uses flat-file format if --output-format is not used.

       --output-format=<type>
	      Specifies format for logging.  Options for <type> are either "xml" or "flat".

       --help Display this help information.

       --version
	      Display the current apbs version.

EXAMPLES

       apbs apbs.in > apbs.out 2> apbs.err

CITATION

       Please cite APBS as follows:

	   Baker  NA,  Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc.
	   Natl. Acad. Sci. USA 98, 10037-10041 2001.

SEE ALSO

       For more information read the user guide and/or the tutorial found online at http://apbs.wustl.edu/.

AUTHORS

       apbs was written by Nathan A. Baker <baker@biochem.wustl.edu>.

       This manual page was written by Daniel Leidert <daniel.leidert@wgdd.de> for the Debian project (but may be used by others).

apbs								     July 2009								   APBS(1)

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)