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)

PSIZE(1)							  PDB2PQR Manual							  PSIZE(1)

NAME

       psize - Get dimensions and other information from PQR files

SYNOPSIS

       psize [--cfact=value] [--fadd=value] [--space=value] [--gememfac=value] [--gememceil=value] [--ofrac=value] [--redfac=value] {pqrfile}

       psize {--help | -h}

DESCRIPTION

       psize derives information from PQR files to preprare the models of proteins and chemicals for electrostatics calculations. The tool
       calculates dimensions for coarse and fine grids, grid spacings, box size and estimates the memory required to perform an electrostatics
       calculation.

       The calculation of this information can be influenced by giving constraints to psize as parameters.

OPTIONS

       psize accepts the following options:

       --help, -h
	   Print a help message and exit.

       --cfact=value
	   Factor by which to expand the molecule dimensions to get the coarse grid dimensions

       --fadd=value
	   Amount to add to the molecule dimensions to get the fine grid dimensions.

       --space=value
	   Desired fine mesh resolution.

       --gememfac=value
	   Number of bytes per grid point required for sequential MG calculation.

       --gememceil=value
	   Maximum MB allowed for sequential MG calculation. Adjust this to force the script to perform faster calculations (which require more
	   parallelism).

       --ofrac=value
	   Overlap factor between mesh partitions.

       --redfac=value
	   Maximum factor by which a domain dimension can be reduced during focusing.

SEE ALSO

       apbs(1), pdb2pqr(1)

AUTHOR

       Manuel Prinz <debian@pinguinkiste.de>
	   Wrote this manpage for the Debian System.

COPYRIGHT

       Copyright (C) 2008 Manuel Prinz

psize								    2008-06-04								  PSIZE(1)