OEFF TK 2.3.0¶
A new generic set of force field potential classes has been added to simplify implementing new force fields in OEFF TK:
With the introduction of the new generic force field potential classes in OEFF TK, several previously existing classes have been deprecated. The following table shows the deprecated classes and their replacements:
Deprecated Class New Class OEMolPotential::OEStretchBase OEStretchPotential OEMolMMFF::OEMMFFStretch OEMolSmirnoff::OESmirnoffStretch OEMolMMFF::OEMMFFBend OEBendPotential OEMolSmirnoff::OESmirnoffBend OEMolMMFF::OEMMFFTorsion OETorsionPotential OEMolSmirnoff::OESmirnoffTorsion OEMolSmirnoff::OESmirnoffOutOfPlane OEOutOfPlanePotential OEMolPotential::OENonBondBase OENonBondPotBase OEMolMMFF::OEMMFFVdw OEVdwPotential OEMolSmirnoff::OESmirnoffVdw OEMolMMFF::OEMMFFCoulomb OECoulombPotential OEMolSmirnoff::OESmirnoffCoulomb OEMolMMFF::OEMMFFInterVdw OEInterVdwPotential OEMolMMFF::OEMMFFInterVdwNN OEMolSmirnoff::OESmirnoffInterVdw OEMolMMFF::OEMMFFInterCoulomb OEInterCoulombPotential
New OpenFF parameters parsley_1.2.1 have been added as built-in parameters and can be used in the construction of an OESmirnoff object.
New FF14SB ([Maier-2015]) protein force field parameters have been implemented. These parameters are accessible through the following parameter and force field classes.
- OEFF14SBSmirnoffParams: an FF14SB for proteins with custom OESmirnoffParams for cofactor and/or ligand
- OEFF14SBParsleyParams: an FF14SB for proteins with OEParsleyParams for cofactor and/or ligand
- OEFF14SBSmirnoff: a force field for proteins with OEFF14SBSmirnoffParams
- OEFF14SBParsley: a force field for proteins with OEFF14SBParsleyParams
- OEFF14SBSmirnoffComplex: a force field for protein-ligand complexes with OEFF14SBSmirnoffParams
- OEFF14SBParsleyComplex: a force field for protein-ligand complex with OEFF14SBParsleyParams
A new class, OEMMFFAmberComplex, has been added that allows protein-ligand optimization with protein flexibility. Accordingly, OEFF::OEMMFFAmber has been deprecated.
A new preliminary class, OEComplexFFParameter, has been added as part of the extended set of OEParameter classes. The new parameter class works with predefined complex force fields using an OEComplexFF object.
A new class, OEComplexEnergies, has been added that represents energy components of a protein-ligand complex.
- All the OEFF TK examples have been reorganized to reflect the modified API behavior.