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
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
ff14sb_parsley, have been added to the -ff command in SZYBKI. The
ff14sb_parsleyis 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
-ffcommand in Freeform -conf.
Major Bug Fixes¶
An issue that delivered incorrect results from binding entropy calculation with SZUBKI, when the
-complexflag 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-Parsleyforce 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-Parsleyforce 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
ELF10partial 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
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
OEFF14SBParsleyComplexforce fields, among others:
A new preliminary class,
OEProteinLigandOptResults, has been added that represents results of a protein-ligand complex optimization.
Two new preliminary classes,
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
OESzybkino longer fails, even when the initial gradient norm is 1e^15 kcal/(mol A) or larger.