Szybki TK 2.2.0

New features

• Two new methods, OESzybkiGeneralOptions::SetForceField and OESzybkiGeneralOptions::GetForceField, have been added that provide support for custom force fields in Szybki TK. These methods provide users with the ability to use SMIRNOFF force fields that are not built into Szybki TK.

• Two new SMIRNOFF force fields from the Open Force Field Initiative, namely Parsley (OpenFF-1.0.0) and Parsley (OpenFF-1.1.1), have been added as built-in force fields. They are defined as OEForceFieldType::PARSLEY_OPENFF100 and OEForceFieldType::PARSLEY_OPENFF111, respectively.

• Potential energy terms in the namespace OEPotentialTerms are now independent of the force field names. Exceptions are combined force fields in which intramolecular terms are taken from MMFF94 as well as intermolecular terms from either AMBER or OEFF.

Major bug fixes

• A bug in the entropy calculation for a ligand inside a receptor binding site has been fixed.

Minor bug fixes

• Conformer free energy calculation using OEFreeFormConf::EstimateFreeEnergies now produces results identical to performing the calculation in steps using the methods from OEFreeFormConfAdvanced.

• The following methods now return bool, instead of a void:

  • OESzybkiGeneralOptions::SetCalculateGradients

  • OESzybkiGeneralOptions::SetIEFFCluster

  • OESzybkiGeneralOptions::SetIntramolecularVdWCutoff

  • OESzybkiGeneralOptions::SetLigandRMSDHeavy

  • OESzybkiGeneralOptions::SetRemoveAttractiveVdWForces

  • OESzybkiGeneralOptions::SetRemoveCoulombTerms

  • OESzybkiGeneralOptions::SetSoluteDielectric

  • OESzybkiGeneralOptions::SetTemperature

  • OESzybkiGeneralOptions::SetVerbose

  • OESzybkiOptOptions::SetCalculateFrozenTerms

  • OESzybkiOptOptions::SetGradTolerance

  • OESzybkiOptOptions::SetMaxIter

  • OESzybkiSolventOptions::SetAtomicRadiiType

  • OESzybkiSolventOptions::SetCavitySolventParameter

  • OESzybkiSolventOptions::SetSaltConcentration

  • OESzybkiSolventOptions::SetSolventDielectric

  • OESzybkiProteinOptions::SetExactVdWProteinLigand

  • OESzybkiProteinOptions::SetIntermolecularVdWCutoff

  • OESzybkiProteinOptions::SetProteinDielectric

  • OESzybkiProteinOptions::SetProteinFlexibilityRange

  • OEFreeFormConfOptions::SetUseInputEnsemble

  • OEFreeFormConfOptions::SetUseSolventCorr

  • OEFreeFormSolvOptions::SetAtomicRadiiType

  • OEFreeFormSolvOptions::SetChargeType

  • OEFreeFormSolvOptions::SetConfGenRMS

  • OEFreeFormSolvOptions::SetIonicState

  • OEFreeFormSolvOptions::SetMaxConfGen

  • OEFreeFormSolvOptions::SetUseInput3D

  • OEFreeFormSolvOptions::SetUseInputEnsemble

• OEForceFieldType::SMIRNOFF has been renamed OEForceFieldType::SMIRNOFF99FROSST for clarity.

• Perceiving residues in the input proteins are now done only when the input protein does not have them.

• Szybki TK now properly handles a hard clash between ligand and protein atoms when a SMIRNOFF force field is used to optimize a ligand inside a receptor (with a gradient norm larger than 1e15).