PDB2PQR 1.2.1 (2007-04) — APBS-PDB2PQR 1.6 documentation

# PDB2PQR 1.2.1 (2007-04)

## 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.
- 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.