New forcefield for ligand-ligand and protein-ligand interactions has been added. It is a combination of MMFF94S (or MMFF94) with intermolecular potential called IEFF developed at OpenEye. In this combined force field, MMFF94S is used to describe the intramolecular interactions while IEFF which has 3 components (vdW, Coulomb and Fermi repulsion) handles intermolecular interactions. Coulomb terms in IEFF require precalculated and assigned atomic multipoles to ligand and protein molecules. This task can be achieved with two OpenEye codes called MOLQM and PROTQM. IEFF has been described in the following publication:
N. Hamaguchi, L. Fusti-Molnar and S. Wlodek Force-field and quantum-mechanical binding study of selected SAMPL3 host-guest complexes J. Comput. Aided Mol. Des. Vol. 26, pp. 577-582, 2012
Please contact email@example.com if you are interested in testing this new forcefield.
New overloaded method OESzybki.SetTorsionConstraint has been added to the public API. It allows selectively constraining a specific torsion in the optimized molecule.
A set of flexible residues in ligand optimization with partially flexible protein is no longer restricted to the specified distance from the ligand. This goal has been achieved by the expansion of the OEProtFlex namespace for new constants which might be passed to the OESz::OESzybkiOptions::SetProteinFlexibilityType method, and the addition of the new method OESz::OESzybkiOptions::AddFlexibleResidue which can be used multiple times to make a set of residues flexible.
Added new virtual method OEOpt::OEFunc1::IsRedundant. It allows to check if two formally numerically different sets of coordinates indeed represent two different points in the coordinate space. This method has no trivial implementation in OEQuatAdaptor.IsRedundant.
MMFF calculations now allow for a “DUMMY” atom type, OEMMFFType.DUMMY to specify that an atom should be avoided during an MMFF energy calculation.
Added a DUMMY atom type to the AMBER force field to specify that an atom should be avoided during an AMBER energy calculation.