Assignment of Forcefield Atom Types

Introduction
Parameter Association
Automatic Forcefield for CFF91 and CVFF

Introduction

The Discover program needs the forcefield atom type of each atom in the molecule or system in order to determine which forcefield parameters to use. The forcefield atom types are related to the chemical environment of the atoms in a way defined by the particular forcefield. For example, a methane molecule has only two atom types, one for the carbon and one for the hydrogens, even though each of the atoms may have a distinct atom name for labeling purposes. The hydrogen atoms are equivalent by symmetry; therefore, they must have the same atom type in any forcefield.

As a more complicated example, consider propane, which has four distinct types of atoms: methyl carbon atoms, methyl hydrogen atoms, a methylene carbon atom, and the methylene hydrogens. In principle, a forcefield could consider these to be four distinct atom types, but in practice, the chemical difference between the carbon atoms or between the hydrogen atoms is very small, so in most forcefields the carbon atoms are all assigned the same atom type, and all the hydrogens are assigned a second atom type.

Atom types must be assigned externally for the Discover program, and it reads the atom type information from the molecular data file (.mdf). The molecular data file and Cartesian coordinate file (.car) are often created in the Insight molecular modeling program, which takes care of assigning the atom types. The Discover program also expects to read partial atomic charges from the .mdf file, because the Discover program has no mechanism for determining these charges. Again, the Insight program is usually used to assign the charges.

Parameter Association

Before calculating the energy of a molecule, the Discover program must associate the forcefield parameters with the appropriate coordinates. For example, methane has one type of bond (C-H) and one type of bond angle (H-C-H). The Discover program must create a list of the four actual bonds and then associate the C-H bond parameters with each. Similarly, there are six H-C-H angles, but they are characterized by the same set of parameters.

It is important to thoroughly understand how the Discover program associates the parameters from the forcefield with individual internal coordinates, because the energy, derivatives, structures, and almost all other properties calculated by the Discover program depend on these forcefield parameters and the way in which they are associated with the internal coordinates. The following sections describe three facets of this process: atom type equivalences, wildcards in parameter definitions, and automatic parameter assignments.

Atom Type Equivalences

Chemically distinct atoms often differ in some, but not all, of their forcefield parameters. For example, the bond parameters for the C-C bonds in ethene and in benzene are quite different, but the nonbond parameters for the carbon atoms are essentially the same. Rather than duplicating the nonbond parameters in the forcefield parameter file, the Discover program uses atom type equivalences to simplify the problem. In the example, the phenyl carbon atom type is equivalent to the pure sp² carbons of ethene insofar as the nonbond parameters are concerned. The Discover program recognizes five types of equivalences for each atom type: nonbond, bond, angle, torsion, and out-of-plane. Cross terms such as bond-bond terms have the same equivalences (insofar as atom types are concerned) as the diagonal term of the topology of all the atoms defining the internal coordinates. For the bond-bond term, this means that the atom type equivalences for angles would be used.

The actual format of the equivalence data in the forcefield parameter file is detailed in the printed Files book. For the equivalences used in any particular forcefield, you should examine the actual forcefield parameter file for up-to-date information.

Wildcard Atom Types in the Parameter File

For some internal coordinates, the parameters do not depend strongly on the specific atom types of one or more atoms. For example, the parameters of the torsional terms are not strongly affected by the end atoms. Physically, this means that the torsion parameters are defined by the central bond rather than its substituents. The Discover program therefore allows wildcard atom types to conveniently handle this type of situation. This special atom type, indicated by an asterisk (*), matches any atom type when the Discover program is searching for the parameters to associate with a particular internal coordinate.

Automatic Forcefield for CFF91 and CVFF

A forcefield may include automatic parameters for use when better-quality explicit parameters are not defined for a particular bond, angle, torsion, or out-of-plane interaction. These parameters are intended as temporary patches, to allow you to begin calculations immediately. While every effort has been made to assure that the automatic parameters in the forcefields supplied by Biosym/MSI (CVFF, CFF91, and ESFF) produce reasonable geometries for a wide variety of molecules, Biosym/MSI cannot guarantee that the automatic parameters will be appropriate in every instance. You therefore should carefully evaluate results obtained using automatic parameters.

Missing parameters in the CFF91 and CVFF forcefields are automatically assigned by switching to an automatic forcefield. This switching is accomplished with an equivalence table that converts the original set of atom types to a smaller set of generic atom types.

In the automatic forcefield, the atom types for bonds, angles, torsions, and out-of-plane deformations have different levels of specificity. For example, while bond-stretching parameters are determined by the atom types of both atoms; angle-bending and torsion parameters may be determined by the atom type of only the central atom(s). A wildcard (*), representing any type of atom, is used for the end atoms of torsions and angles.

In some cases, angle-bending parameters are specified by two atoms (rather than only the central atom). This can lead to ambiguity-for example, C-C-N can be associated with c_-c_-* or with n_-c_-*. The underscore in this example is used to denote the generic (or automatic) atom types. Here, a one-sided wildcard (*#, where # is an integer indicating the precedence), is used for one of the end atoms in an angle. The parameters for a C-C-N angle would be taken from those for atom types n_-c_-*6 rather than c_-c_-*7, because 6 is smaller than 7.

As an example, the parameters for the angle oh-c"-c" in oxalic acid (Figure 3-1) are not present in CFF91.

When the automatic parameter assignment process is used, it looks at the auto-equivalence table in the cff91.frc file to find the generic atom types for this angle (indicated in bold type):

#auto_equivalence     cff91_auto

!                          Equivalences
!            -----------------------------------------------------------------------------
!Ver Ref Type NonB Bond Bond  Angle     Angle    Torsion     Torsion      OOP       OOP
!                  Inct     End Atom  Apex Atom End Atoms  Center Atoms End Atom Center Atom
!--- --- ---- ---- ---- --- -------- ---------- ---------- ------------ -------- -----------
 2.0  2   c"   c"   c"   c'_    c_        c'_       c_          c'_       c_        c'_
 2.0  2   oh   o    o_   o_     o_        o_        o_          o_        o_        o_

Thus, atom type oh is reassigned to o_, c" is reassigned to c'_ for the apex atom, and c" is reassigned to c_ for the end atom. The parameters for the oh-c"-c" angle are taken from the o_ c'_ *7 line in the quadratic_angle section of the cff91.frc file:

#quadratic_angle      cff91_auto

> E = K2 8 (Theta - Theta0)^2

!Ver  Ref     I      J      K       Theta0         K2
!---- ---   ----   ----   ----   ---------    ---------
 2.0   2      c_     c'_    *9    120.0000       40.0000
 2.0   2      n_     c'_    *8    120.0000       53.5000
 2.0   2      o_     c'_    *7    110.0000      122.0000
 2.0   2      o'_    c'_    *f    120.0000       68.0000
 2.0   2      h_     c'_    *2    110.0000       55.0000

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