Calculation of the constant potential terms at the end of adapted
optimization can be optionally eliminated, by the use of the
-neglect_frozen flag. This feature allows for less memory
and cpu usage in the case of partial optimization of large
The corresponding atom symbols, bond symbols, and torsion angles
are now printed on a line under the matching smarts pattern.
Input proteins with only partial information about residues were not
handled properly. As a result, none of the side chains which were
supposed to be made flexible with the use of an option -sideC
were optimized. This problem was fixed.
A bug causing memory corruption in the case of ligand optimization
in partially flexible protein receptor is fixed.
Residues with non-standard name CYX were not properly handled in
the situation when their side chains were included into the
flexible part of the protein receptor. This bug has been fixed.