Added the mcce.py module to subdirectory "mccetools"
Fixed some FFAMBER residue naming issues (thanks, Sanghyun)
Adding more documentation in mcce.py, and fixing a minor bug that required the "pdb file" name actually to be an absolute path.
More DLM edits to documentation.
Fixing a bug that caused the terminal oxygens not to be named correctly.
Removed an extra print statement.
Added Greg/John's modellertools to project.
Added latest version of mccetools, with example script for protonating a PDB file with the correct pKa states.  WARNING: the pKas calculations are untested are probably incorrect.
Fixed __init__.py
Rebuilt Wing project file to update directories.

Selected the following:

* Options -> Project Type to "Shared (Two Files)". See http://www.wingware.com/doc/proj/project-types  -- this means that the .wpr file contains only shared data, and we can fiddle with other non-shared data in the .wpu files.
* Extensions -> Enable Revision Control and set Revision Control System to "subversion" (SVN).
Creates PDB model given template PDB and target sequence
Added MCCE install instructions
Added gromacstools
removed extraneous file
Added utilities/ directory with Constants and Units classes.
Added __init__.py to utilities/ directory.

Auto-reformatted spaces/tabs issue in ioncalc.py -- hope nothing broke!
Added many comments and some docstrings to ioncalc.  I have not tested it -- not sure it still works.
Minor additional comment to ioncalc.py. Still have not tested.
Updated comments on how to use Units class.
More updates to comments.