The combination of options -complexif1 and -ligandsif2 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 -complexif1 and -ligandsif2 is used.
Redundant warnings generated upon -protein_elecnone 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
Examples of log files generated upon ligand optimization in the
partially flexible protein followed by a single point PB
calculations are given.