Szybki TK 1.8.7¶
OESzybkiEnsembleResults.HasEntropyhas been added. This new method returns
falsewhenever a requested entropy calculation fails.
The default behavior of protein-ligand systems handled with MMFF or MMFF_AMBER force fields has changed from
OEProteinElectrostatics.ExactCoulomb. In other words, Coulomb protein-ligand interactions are included by default. Beginning with this release, removing Coulomb terms from the protein-ligand interactions requires using the
OESz::OESzybkiOptions::SetProteinElectrostaticModelmethod with the
Previously, the combination of IEFF force field and PB desolvation was restricted to using ESP charges calculated along with atomic multipoles. This restriction has been removed and IEFF for protein-ligand interaction can now be used together with the method
Major bug fixes¶
Return values of the methods
OESz::OESzybkiOptions::SetProteinFlexibilityRangehave been changed from
bool. This change allows for verifying whether the options have been successfully set.
When IEFF force field is selected, implying that molecular input files with pre-calculated atomic multipoles have been used, the addition of explicit hydrogens is now disabled. In very rare cases (for example, tetracyanoquinodimethane ligand), perception of bonding might not correspond to the actual ab-initio pre-calculated structure, causing the IEFF calculated energies to be incorrect.
Using external charges (see method
OESz::OESzybkiOptions::SetUseCurrentCharges) in the
OEForceFieldType.MMFF_AMBERforce field for protein-ligand Coulomb interactions was failing unless the protein was eligible for correct AMBER charging. This unnecessary condition has been removed: any atomic preassigned atomic charges can now be used in combination with AMBER vdW protein-ligand interactions.
Entropy calculation at very low temperatures is now handled properly: at 0 Kelvin, a value of zero is always returned. At temperatures close to 0 Kelvin, calculation is attempted and a warning is issued if the calculation fails.
OESzybkiEnsembleResults.HasEntropy(see above) might be used to query if the
OESzybkiResultsobject contains valid calculated entropy.
Using IEFF/PB potential for bound ligand optimization in torsion space when the ligand receptor is partially flexible did not always work. This issue has been fixed.
Minor bug fixes¶
When attempting to use Newton optimization and IEFF force field results, an error is now thrown with the message “Second derivatives not available for IEFF ff”.