- The combination of options -complex if1 and -ligands if2 run in the pvm mode caused incorrect behavior in the case when the preexisting ligand in the macromolecule (in the file if1) overlapped with one or more ligands from the input file if2.
- Run time license for the shape toolkit is added. It is required when the combination of options -complex if1 and -ligands if2 is used.
- Redundant warnings generated upon -protein_elec none and -strip_water were removed.
- Spelling in the log file was fixed.
- Year 2008 was added to the Szybki banner.
- In the documentation description for the -fix_smarts option an example was added which illustrates the adjustment of hydrogen atom positions.
- Examples of log files generated upon ligand optimization in the partially flexible protein followed by a single point PB calculations are given.