OBForceFieldMMFF94

From Open Babel

This class is a partial implementation of the all-atom MMFF94 force field.

References:

1. Thomas A. Halgren, J. Comput. Chem., 17, 490-519 (1996).
2. Thomas A. Halgren, J. Comput. Chem., 17, 520-552 (1996).
3. Thomas A. Halgren, J. Comput. Chem., 17, 553-586 (1996).
4. Thomas A. Halgren and Robert B. Nachbar, J. Comput. Chem., 17, 587-615 (1996).
5. Thomas A. Halgren, J. Comput. Chem., 17, 616-641 (1996).
6. Thomas A. Halgren, J. Comput. Chem., 20, 720-729 (1999).
7. Thomas A. Halgren, J. Comput. Chem., 20, 730-748 (1999).

The intent in the future is to produce a full, validated MMFF94 implementation.

Contents 1 Use 2 Parameters 3 Functional form 3.1 Bond Stretching 3.2 Angle Bending 3.3 Bend Stretching 3.4 Torsional 3.5 Out-Of-Plane Bending 3.6 Van der Waals 3.7 Electrostatic 4 Validation

Use

The MMFF94 force field can be used for organic molecules and biomolecules. It describes non-bonded interactions between a ligand and protein very wel, this makes MMFF94 suitable for docking.

Parameters

The MMFF94 parameters can be found in the data/mmff*.par files.

Functional form

Bond Stretching

(1)

: bond stretching force constant (mmffbond.prm)

: ideal bond length (mmffbond.prm)

: bond length between atoms a and b

: cubic stretching constant (-2.0)

Angle Bending

(2)

: angle bending force constant (mmffang.prm)

: ideal angle (mmffang.prm)

: angle

: cubic bending constant (-0.007)

Bend Stretching

(3)

: angle bending force constant (mmffang.prm)

: ideal angle (mmffang.prm)

: angle

: cubic bending constant (-0.007)

Torsional

Out-Of-Plane Bending

(5)

Van der Waals

Electrostatic

Validation

The validation is done using the MMFF94 validation suite. The output from OBForceFieldMMFF94::Validate() can be found here. There are still minir errors for the stretch-bending terms. The analytical gradients have also been implemented and their values are validated by comparing them to numerical derivatives.