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BETA PUBLIC RELEASE VERSION 1.2.1       4-1-07
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  - NEW FEATURES
    * Updated documentation to include instructions for pdb2pka support,
      references, more pydoc documents.
    * Added ligand examples to examples/ directory
    * Added native support for the TYL06 forcefield.  For more information
      on this forcefield please see
        Tan C, Yang L, Luo R.  How well does Poisson-Boltzmann implicit
        solvent agree with explicit solvent? A quantitative analysis.
        Journal of Physical Chemistry B.  110 (37), 18680-7, 2006.1
    * Added a new HTML output page which relays the different atom types
      between the AMBER and CHARMM forcefields for a generated PQR file
     (thanks to the anonymous reviewers of the latest PDB2PQR paper).

  - BUG FIXES
    * Fixed bug where a segmentation fault would occur in PropKa if the N
      atom was not the first atom listed in the residue
    * Fixed error message that occurred when a blank line was found in a
      parameter file.
    * Better error handling in MOL2 file parsing.
    * Fixed bug where ligands were not supported on PDB files with multiple
      MODEL fields.
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BETA PUBLIC RELEASE VERSION 1.2.0       1-31-07
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  - NEW FEATURES
    * Added autoconf support for pdb2pka directory.
    * Added new support for passing in a single ligand residue in MOL2 format
      via the --ligand command.  Also available from the web server (with link
      to PRODRG for unsupported ligands).
    * Numerous additions to examples directory (see examples/index.html) and 
      update to User Guide.
  - BUG FIXES 
    * Fixed charge assignment error when dealing with LYN in AMBER.
    * Fixed crash when a chain has a single amino acid residue.  The code
      now reports the offending chain and residue before exiting.
    * Fixed hydrogen optimization bug where waters with no nearby atoms at
      certain orientations caused missing hydrogens.
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BETA PUBLIC RELEASE VERSION 1.1.2       6-23-06
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  - BUG FIXES 
    * Fixed a bug in the hydrogen bonding routines where PDB2PQR attempted to 
      delete an atom that had already been deleted. (thanks to Rachel Burdge)
    * Fixed a bug in chain detection routines where PDB2PQR was unable to
      detect multiple chains inside a single unnamed chain (thanks to 
      Rachel Burdge)
    * Fixed a second bug in chain detection routines where HETATM residues
      with names ending in "3" were improperly chosen for termini (thanks to
      Reut Abramovich)
    * Fixed a bug where chains were improperly detected when only containing
      one HETATM residue (thanks to Reut Abramovich)
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BETA PUBLIC RELEASE VERSION 1.1.1       5-3-06
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  - BUG FIXES 
    * Fixed a bug which prevented PDB2PQR from recognizing atoms from nucleic 
      acids with "*" in their atom names. (thanks to Jaichen Wang)
    * Fixed a bug in the hydrogen bonding routines where a misnamed object
      led to a crash for very specific cases. (thanks to Josh Swamidass) 
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BETA PUBLIC RELEASE VERSION 1.1.0       4-12-06
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  - NEW FEATURES
    * Structural data files have been moved to XML format.  This should make 
      it easier for users and developers to contribute to the project.
    * Added an extensions directory for small scripts.  Scripts in this 
      directory will be automatically loaded into PDB2PQR has command line
      options for post-processing, and can be easily customized.
    * Code has been greatly cleaned so as to minimize values hard-coded
      into functions and to allow greater customizability via external
      XML files.  This includes a more object-oriented hierarchy of
      structures.
    * Improved detection of the termini of chains.
    * Assign-only now does just that - only assigns parameters to atoms
      without additions, debumping, or optimizations.
    * Added a --clean command line option which does no additions,
      optimizations, or forcefield assignment, but simply aligns the PDB
      columns on output.  Useful for using post-processing scripts like
      those in the extensions directory without modifying the original input
      file.
    * The --userff flag has been replaced by opening up the --ff option
      to user-defined files.
    * Pydoc documentation is now included in html/pydoc.
    * A programmer's guide has been included to explain programming decisions
      and ease future development.
    * A --ffout flag has been added to allow users to output a PQR file in
      the naming scheme of the desired forcefield.
    * User guide FAQ updated.
    * The efficiency of the hydrogen bonding detection script (--hbond) has 
      been greatly improved. 
    * Increased the number of options available to users via the PDB2PQR
      web server.
  - BUG FIXES
    * Updated psize.py to use centers and radii when calculating grid sizes
      (thanks to John Mongan)
    * Fixed bug where PDB2PQR could not read PropKa results from chains with
      more than 1000 residues (thanks to Michael Widmann)
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BETA PUBLIC RELEASE VERSION 1.0.2       12-15-05
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  - NEW FEATURES
    * Added ability for users to add their own forcefield files.  This
      should be particularly useful for HETATMs.
    * Added sdens keyword to inputgen.py to make PDB2PQR compatibile with
      APBS 0.4.0.
    * Added a new examples directory with a basic runthrough on how to use
      the various features in PDB2PQR.
  - BUG FIXES 
    * Fixed a bug that was unable to handle N-Terminal PRO residues with
      hydrogens already present.
    * Fixed two instances in the PropKa routines where warnings were 
      improperly handled due to a misspelling.
    * Fixed instance where chain IDs were unable to be assigned to proteins
      with more than 26 chains.
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BETA PUBLIC RELEASE VERSION 1.0.1       10-7-05
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  - NEW FEATURES
    * Added citation information to PQR output.
  - BUG FIXES 
    * Fixed a bug during hydrogen optimization that left out H2 from water
      if the oxygen in question had already made 3 hydrogen bonds.
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BETA PUBLIC RELEASE VERSION 1.0.0       8-23-05
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This is the initial version of the PDB2PQR conversion utility.  There are 
several changes to the various "non-official" versions previously available:
    * SourceForge has been chosen as a centralized location for all
      things related to PDB2PQR, including downloads, mailing lists,
      and bug reports.
    * Several additions to the code have been made, including pKa support
      via PropKa, a new hydrogen optimization algorithm which should 
      increase both accuracy and speed, and general bug fixes.

We plan on continuing to improve PDB2PQR by refining the code, adding more
advanced options, and encouraging collaborations with other utilities.

Thank you for your time and interest in the PDB2PQR software.
