OEMMFFAmber

Attention

This API is currently available in C++ and Python.

class OEMMFFAmber : public OEMolPotential::OEGenericFF2

A hybrid force field that applies MMFF intramolecular terms to the ligand and Amber intramolecular terms to the host (protein), with Amber-based intermolecular interactions between them. This force field is intended for use in protein-ligand scoring and optimization workflows.

The host molecule must have 3D coordinates assigned. The ligand must have 3D coordinates and partial charges assigned (e.g. via OEAssignCharges) before calling PrepMol.

See also

• OEMMFFAmberOptions class

• OEMMFFAmberComplex class

The following methods are publicly inherited from OEFunc0:

• operator()

• GetFComponents

• NumVar

The following methods are publicly inherited from OEFunc1:

• operator()

The following methods are publicly inherited from OEFunc2:

• operator()

The following methods are publicly inherited from OEMolFunc:

• Clear

• ClearPredicates

• GetInteractions

• Setup

The following methods are publicly inherited from OEForceField:

• PrepMol

• Set

The following methods are publicly inherited from OEGenericFF2:

• AddMolFunc

• GetComponents

• RemoveMolFunc

The OEMMFFAmber class defines the following public methods:

• PrepMol

• Setup

Constructors

OEMMFFAmber(const OEChem::OEMolBase& host)

Constructs the force field using the given host molecule and default OEMMFFAmberOptions.

OEMMFFAmber(const OEChem::OEMolBase& host,
            const OEMMFFAmberOptions& options)

Constructs the force field using the given host molecule and the specified options.

operator=

OEMMFFAmber & operator=(const OEMMFFAmber &)

Assignment operator.

PrepMol

bool PrepMol(OEChem::OEMolBase& mol, bool sweep = true,
             bool warnOK = true) const

Prepares a ligand molecule for use with this force field by assigning MMFF atom types and partial charges. Returns true on success.

sweep

If true, sweeps through charge models to find one that covers all atoms.

warnOK

If true, suppresses warnings for atoms that cannot be typed.

Setup

bool Setup(const OEChem::OEMolBase& mol)

Sets up the force field for the given ligand molecule. The molecule must have been prepared with PrepMol before calling this method. Returns true on success.