SZYBKI 2.3.0.2¶

March 2021

A new parameter, -proteinMask, has been added to both OptimizeDU and OptLigandInDU to provide flexibility in identifying the target protein components of a design unit for optimization.

SZYBKI 2.3.0.0¶

Fall 2020

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.

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.

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.

Fall 2020

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 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, among others:
- OEFixedProteinLigandOptimizer
- OEFlexProteinLigandOptimizer
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.

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.