Calculation of the constant potential terms at the end of adapted optimization can be optionally eliminated, by the use of the
-neglect_frozenflag. This feature allows for less memory and cpu usage in the case of partial optimization of large molecules.
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
-sideCwere 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 nonstandard name
CYXwere 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.