- A new utility, OptLigandInDU, has been added that optimizes a ligand against a rigid protein active site in a design unit. Optimization can be performed with fff14sb_parsley, mmff_amber, or mmff force fields.
- A new utility, OptimizeDU, has been added that optimizes a protein-ligand complex inside a design unit. The protein can be treated as partially flexible during the optimization, and can be performed with fff14sb_parsley, mmff_amber, or mmff force fields.
- New options, parsley_openff1.2.1 and ff14sb_parsley, have been added to the -ff command in SZYBKI. The ff14sb_parsley is only meaningful when optimizing a protein or a part of a protein that includes cofactors.
- A new option, parsley_openff1.2.1, , has been added to the -ff command in Freeform -conf.
Major Bug Fixes¶
- An issue that delivered incorrect results from binding entropy calculation with SZUBKI, when the -complex flag was used has been fixed.
- Depiction of Freeform -solv results now shows the breakdown of group contributions.
Minor Bug Fixes¶
- Protein-ligand optimization with OpenFF-Parsley force fields using SZYBKI no longer fails even when the initial gradient norm is 1e15 kcal/(mol A) or larger.
- The SZYBKI log file for protein-ligand complexes optimized with OpenFF-Parsley force fields no longer provides the misleading message mmff94 partial charges were used.
- The log file for default Freeform -conf calculations that runs with default charges has been improved to correctly say that the ELF10 partial charges were used.
- Unnecessary warnings in entropy calculations with SZYBKI have been removed.
Szybki TK 2.3.0¶
- A new SMIRNOFF force field from the Open Force Field Initiative, Parsley 1.2.1, has been added as a built-in force field. It is defined as OEForceFieldType::PARSLEY_OPENFF121.
- A protein or part of a protein can now be optimized with the FF14SB force field. Cofactors with the exception if HEME are handled by the OpenFF/Parsley force field (for example Parsley 1.2.1), while parameters for HEME are taken from Bryce Group.
- The following preliminary classes have been added that enable optimizing protein-ligand complexes,
with or without partial flexibility of the proteins, using the new OEFF14SBParsleyComplex force fields,
- A new preliminary class, OEProteinLigandOptResults, has been added that represents results of a protein-ligand complex optimization.
- Two new preliminary classes, OEProteinLigandOptOptions and OEProteinFlexOptions, have been added that provide choices for protein-ligand optimization and protein flexibility.
- A new namespace, OESzybkiReturnCode, and a corresponding function, OEGetSzybkiError, have been added that correspond to return codes from the new optimizer classes.
Minor bug fixes¶
- Protein-ligand optimization with OpenFF/Parsley force fields using OESzybki no longer fails, even when the initial gradient norm is 1e^15 kcal/(mol A) or larger.