SZYBKI 2.5.1

Fall 2022

New features

  • Output for freeform -calc conf now adds dG, local strain, and global strain values to tracked conformer output files as SD data.

Minor bug fixes

Szybki TK 2.5.1.2

Szybki TK 2.5.1.1

New features

  • Optimization of bound ligands with ff14SB/Sage and ff14SB/Parsley force fields with PB solvation forces in rigid and partially flexible receptors is now available.

  • Setting the force field to PARSLEY_OPENFF131 or SAGE_OPENFF200 now references the most recent official versions of those two parameterizations which are OpenFF_1.3.1 and OpenFF_2.0.0 respectively. Older versions are still available from the OEForceFieldType namespace.

  • Final ligand geometry is now checked when large initial clashes occur while using OEFixedProteinLigandOptimizer and OESz_OEFlexProteinLigandOptimizer for optimization of a ligand inside a protein receptor. In most cases, clashes are successfully relaxed; however, in some cases they can lead to a non-physical minimum which is characterized with distorted geometry. Such results can now be detected by checking the return values of methods OEFixedProteinLigandOptimizer_Optimize and OEFlexProteinLigandOptimizer_Optimize.

Major bug fixes

  • An issue with torsion scan for alkanes using MMFF has been fixed.

  • OEFixedProteinLigandOptimizer_Optimize and OEFlexProteinLigandOptimizer_Optimize now fails properly when optimization leads to a non-physical state of a molecule, characterized with distorted geometry. Such non-physical optimization can sometimes happen when the starting configuration of a protein-ligand complex contains high overlaps.

Minor bug fixes