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.

A misleading error message produced by SZYBKI when run with freeform -ff ieff_mmff94 or freeform -ff ieff_mmff94s, without specifying the receptor with either szybki -protein or szybki -complex, has been improved.
Values of dG, local strain, and global strain have been added to the tracked_rst file when freeform is run with the freeform -track option.
Case-insensitive values for freeform -ff are now accepted in SZYBKI.

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 nonphysical 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.

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 nonphysical state of a molecule, characterized with distorted geometry. Such nonphysical optimization can sometimes happen when the starting configuration of a protein-ligand complex contains high overlaps.

A warning regarding ‘invalidation of receptor’ upon optimization using the OEFlexProteinLigandOptimizer class has been removed.