README for tools/conversion/pdb2pqr directory
---------------------------------------------

Authors: Todd Dolinsky (todd@ccb.wustl.edu)
Portions based on C code by Jens Erik Nielsen

Date: 1/15/2004

This directory contains a pdb2pqr script which allows a user to
convert a standard PDB file to a PQR file using the amber, charmm,
or parse forcefields.

Usage:

Usage: pdb2pqr.py [options] --ff=<forcefield> <path> [output-path]
    Required Arguments:
        <path>        :  The path to the PDB file or an ID
                         to obtain from the PDB archive
        <forcefield>  :  The forcefield to use - currently
                         amber, charmm, and parse are supported.
    Optional Arguments:
        --verbose (-v):  Print information to stdout
        --help    (-h):  Display the usage information
    If no output-path is specified, the PQR file is printed to stdout

Notes:
    At this time, the script will only assign charges and radii to atoms
    present in the PDB file - in the future it will be able to detect
    missing atoms and rebuild them, add hydrogens and optimize the entire
    protein.

    PDB files without hydrogens will generate a long list of warning messages 
    about non-integral charges for residues - this is due to the missing 
    hydrogens, and thus can be expected.  Any warnings that PDB2PQR
    was unable to assign a charge to a non-HETATM heavy atom should be
    addressed before proceeding - it may be a naming issue not handled 
    within the script.


If you would like to automatically generate an input file from the new PQR
file, please see

apbs/tools/manip/inputgen.py
