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Article ID: 1266 - Last Modified: April 7, 2011

MacroModel contains a variety of force fields. Which is best for my purpose?

Each of the MacroModel force fields has strengths, but in general, the most complete and well parameterized force fields are MMFF, OPLS_2001, and OPLS_2005. The other force fields are routinely used for special situations; for example, when using united atoms (AMBER*) or when reproducing or extending previous results. Although there are no absolute guidelines available for choosing the most appropriate MacroModel force field for a given molecular modeling application, the following generalizations are reasonable:

OPLS_2005: Probably the best available force field for condensed-phase simulation of peptides. Work to develop parameterization that will include broader classes of drug-like molecules is ongoing.

OPLS_2001: Is a solid implementation of the OPLS-AA force field. GB/SA solvation energies are good.

MMFF: An excellent force field for biopolymers and many organic molecules that do not have parameters in other force fields. The MMFFs extension of this force field is also supported.

AMBER*/OPLS*: Good force fields for biopolymers and carbohydrates; we have added many parameters which extend the scope of this force field to a number of important organic functional groups. GB/SA solvation energies range from moderate (AMBER*) to good (OPLS*).

AMBER94: An excellent force field for proteins and nucleic acids. However, there are no extensions for non-standard residues or organic molecules.

MM2*/MM3*: Excellent force fields for hydrocarbons and molecules with single or remotely spaced functional groups. GB/SA solvation energies tend to be poor relative to those calculated with other force fields.

Often when choosing a force field, you can use as a guide the parameter quality that is reported in the log file for the calculation. If you are using a force field for which many warnings about low-quality parameters are issued, particularly for torsion parameters, you may want to try one or two of the other force fields to see if they are better parameterized. Note, however, that because functional group interaction is so complex, no force field has parameters for everything. Also note that the presence of high-quality parameters alone does not guarantee that the potential energy surface is being accurately modeled.

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