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 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.