- 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.
- 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.