Suplementary Material for: "Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization and Performance of MMFF94," T. A. Halgren, J. Comp. Chem., 17, 490-519 (1996).
MMFF94 uses fifteen "regular" parameter" files and an optional sixteenth file that supplies additional or replacement parameters for various terms in the energy expression (eq 1). Complete versions of the first fifteen parameter files (core plus extended paramaterization) and a particular example of the sixteenth file are available via in ASCII format [1]. This appendix will identify the role each parameter file plays and reference the paper in which the information contained therein is illustrated and discussed. The supplementary-parameters file MMFF93SUP.PAR provides the modified out-of-plane and torsion parameters needed to reconstitute the earlier "MMFF93" version [2] of the force field.
1. MMFFSYMB.PAR. This file specifies the four-character symbolic atom types used in MMFF94, defines the numeric atom type to which each corresponds, and gives a qualitative description of the chemical environment that each represents. Note that the symbolic to numeric correspondence in general is many to one, and that the numeric atom types are the ones used in matching parameters to force-field interactions. The contents of this file appear in Table III of this paper.
2. MMFFDEF.PAR. This file supplies the atom type equivalences used in the matching of parameters to force-field interactions described in the section on "Implementation of MMFF ...". The contents of this file are listed in Table IV of this paper.
3. MMFFAROM.PAR. For non-hydrogen atoms, the assignment of symbolic MMFF atom types takes place in two stages. In the first, a provisional atom type is assigned based on local connectivity. In the second, aromatic systems are perceived, and properly qualified aromatic atom types are assigned based on ring size and, for five-membered rings, on the position within the ring. Information in this file is used to make the proper correspondence between provisional and final (aromatic) atom types. As this file is not described in any of the papers in this series, we give an excerpt below:
* * Copyright (c) Merck and Co., Inc., 1994, 1995 * All Rights Reserved * * MMFF AROMATIC SYMBOLIC TYPES VS ORIGINALLY ASSIGNED TYPES * * OLD AROM AT RING IM N5 *TYPE TYPE NUM SIZE L5 CAT ANION C* CB 6 6 0 0 0 N* NPYD 7 6 0 0 0 NCN+ NPD+ 7 6 0 0 0 N+=C NPD+ 7 6 0 0 0 N=+N NPD+ 7 6 0 0 0 N2OX NPOX 7 6 0 0 0 * C* C5A 6 5 2 0 0 C* C5B 6 5 3 0 0 C* C5 6 5 4 0 0 N* NPYL 7 5 1 0 0 N* N5A 7 5 2 0 0 N* N5B 7 5 3 0 0 N* N5 7 5 4 0 0 CNN+ CIM+ 6 5 2 1 0 CNN+ CIM+ 6 5 3 1 0 CNN+ CIM+ 6 5 4 1 0As in all the MMFF parameter files, lines beginning with a "*" are comment lines. The column labeled "L5" refers, in the case of 5-ring systems, to the position of the atom in question relative to the unique pi-lone-pair containing heteroatom (which itself occupies position "1"); a "4" is an artificial entry that is assigned when no such unique heteroatom exists, as for example occurs in imidazolium cations and in tetrazole anions. An entry of "1" in the "IM CAT" or "N5 ANION" column must also be matched for such ionic species to convert the "OLD" (preliminary) to "AROM" (aromatic) symbolic atom type. Note: in matching the "OLD" symbolic atom types, an "exact" match is first attempted. If this match fails, a wild-carded match, using for example "C*" is then employed.
4. MMFFHDEF.PAR. Symbolic atom types for hydrogen atoms are derived from the atom types of the parent non-hydrogen to which each is attached (a special hard-coded provision is made for recognizing molecular hydrogen). This file provides the information needed to make the proper correspondence. It lists the MMFF symbolic atom type for the parent atom and the symbolic atom type to be assigned to the attached hydrogen.
5. MMFFPROP.PAR. This file specifies the chemical and geometric properties associated with each of the numeric MMFF atom types. This information is described in the "MMFF94 Atom Types and Associated Properties" section of Paper V[3]. The contents of the file are displayed in Table I of that paper.
6. MMFFBOND.PAR. This file supplies parameters for bond-stretching interactions. An abridged version is given in Table III of Paper III [4].
7. MMFFBNDK.PAR. This file supplies parameters used in the empirical rule for bond-stretching force constants discussed in the "Extension of Parameterization for Bond Stretching" section of Paper V [3]. These empirical-rule parameters are listed in Table V of that paper.
8. MMFFANG.PAR. This file supplies parameters for angle-bending interactions. An abridged version is given in Table IV of Paper III [4].
9. MMFFSTBN.PAR. This file supplies parameters for stretch-bend interactions. An abridged version is given in Table V of Paper III [4].
10. MMFFDFSB.PAR. This file supplies default parameters for stretch-bend interactions that are used when specific parameters are not found in the MMFFSTBN.PAR file. See the "Extension of Parameterization for Stretch-Bend Interactions" section and Table VII of Paper V [3].
11. MMFFOOP.PAR. This file supplies parameters for out-of-plane bending interactions. An abridged version is given in Table VI of Paper III [4].
12. MMFFTOR.PAR. This file supplies parameters for torsion interactions. An abridged version is given in Table V of Paper IV [2].
13. MMFFVDW.PAR. This file supplies parameters for van der Waals interactions. An abridged version is given in Table III of Paper II [5].
14. MMFFCHG.PAR. This file supplies bond-charge-increment parameters used to construct the partial atomic charges employed in calculating electrostatic interactions. An abridged version is given Table IV of Paper II [5].
15. MMFFPBCI.PAR. This file supplies "partial-bond-charge-increment" parameters used in the empirical rule for bond-charge-increment parameters described in the "Extension of Parameterization for Electrostatic Interactions" section of Paper V [3]. It also specifies the "formal charge sharing" parameters discussed in the same section of that paper. The file contents are listed in Table III of the same paper.
16. MMFF93SUP.PAR. This file provides the values used for two out-of-plane and seventy-one torsion parameters in the earlier "MMFF93" version of the MMFF force field.
[2] Paper IV: T. A. Halgren and R. B. Nachbar, J. Comput. Chem., 17, 587-615 (1996).
[3] Paper V: T. A. Halgren, J. Comput. Chem., 17, 616-641 (1996).
[4] Paper III: T. A. Halgren, J. Comput. Chem., 17, 553-586 (1996).
[5] Paper II: T. A. Halgren, J. Comput. Chem.,17, 520-552 (1996).