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

New Features

  • 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

Fall 2020

New features

  • 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, 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.

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.