Tripos Force Field (TAFF)


The parameters for the Tripos Force Field (TAFF) are not part of the Wit!P distributions. Without these parameters, the Wit!P command TAFF (to generate X-Plor input files using TAFF) and the external program Minimax  will not work. If you have access to Tripos's Sybyl software, you may use Sybyl's parameter ascii write command to generate a set of files with TAFF parameters in a format which is readable by Wit!P. Alternatively, you may generate your own set of parameter files from the tables in [1]. The complete parameter set consists of 7 files:

ATOM_DEF: information about TAFF atom types. Free-format file, with one line per atom type. For reasons of compatibility with Sybyl's parameter ascii format, each line must contain 17 fields. In Wit!P only a subset of these fields is used. A '-' may be used as a place holder for the unused fields. If the first character of a line is '#', the whole line will be treated as comment.
 
Field Label Comment
1 mnem atom type name, should match type definition in Wit!P library file all.wlb
2 elt chemical element
5 equiv equivalent type (c.f. parameter assignment rules).
6 Z atomic number
11 HBdon? YES, if atom is a potential HB donor, NO otherwise
12 HBacc? YES, if atom is a potential HB acceptor, NO otherwise
16 num.type numeric type, should match n in corresponding type definition in all.wlb

Example: ATOM_DEF record for the TAFF C.cat atomtype:

C.cat C - - C.2 6 - - - - NO NO - - - 33 -


BOND_DEF: definition of bond types. Free-format file, with one line per bond type. For compatibility reasons, the file must contain 6 fields per bond type. Only 3 of these fields are used in Wit!P. A '-' may be used as a place holder for the unused fields. If the first character of a line is '#', the whole line will be treated as comment.
 
Field Label Comment
1 mnem bond type name
2 num.type numeric bond type (used in old .mol files)
4 real? YES, if this is a chemical bond, NO for dummy and non chemical bonds

Currently, Wit!P uses the following bond types:
 
bond type mnemonic num.type real?
single 1 1 YES
double 2 2 YES
triple 3 3 YES
amide am 4 YES
aromatic ar 5 YES
dummy du 8 NO
unknown un 9 NO
non chemical nc 10 NO

Example: BOND_DEF record for the double bond type:

  2 2 - YES - -


TAFF_BOND_STRETCH: contains parameters for the harmonic bond stretch term. Lines that start with the '#' character are treated as comment. Each non-comment line contains the following fields:
 
Field Label Comment
1 atm1 1st atom type, from ATOM_DEF, or * wild card
2 atm2 2nd atom type, from ATOM_DEF, or * wild card
3 btype bond type, from BOND_DEF
4 r0 equilibrium bond length (Å)
5 k force constant (Kcal mol-1 Å-2)
6 source comment, e.g. TAFF5.2, guess, ... 

Example: "guesstimated" B.3-O.3 single bond stretch parameter

B.3 O.3 1 1.540 200.00 A.Widmer


TAFF_ANGLE_BEND: contains parameters for the harmonic angle bend terms. Lines that start with the '#' character are treated as comment. Each non-comment line contains the following fields:
 
Field Label Comment
1 atm1 1st neighbor, from ATOM_DEF, or * wild card 
2 atm2 central atom, from ATOM_DEF, or * wild card
3 atm3 2nd neighbor, from ATOM_DEF, or * wild card
4 w0 equilibrium angle (degrees)
5 k force constant (Kcal mol-1 degree-2)
6 source comment, e.g. TAFF5.2, guess, ...

Example: "guesstimated" C.3-B.3-O.3 angle bend parameter:

C.3 B.3 O.3 116.20 0.020 A.Widmer


TAFF_OOP_BEND: contains parameters for the harmonic out-of-plane terms. If the first character of a line is '#', the whole line will be treated as comment. If the first character of a line is '#', the whole line will be treated as comment.
 
Field Label Comment
1 atm atom type of central atom
2 k force constant (Kcal mol-1 Å-2)
3 source comment, e.g. TAFF5.2, guess, ...

Example: slightly improved (compared to TAFF5.2) oop parameter for aromatic carbon:

C.ar 625.00 A.Widmer


TAFF_TORS: contains parameters for the torsion potential. If the first character of a line is '#', the whole line will be treated as comment. If the first character of a line is '#', the whole line will be treated as comment.
 
Field Label Comment
1 atm1 atom type, or * wild card
2 atm2 atom type, or * wild card
3 atm3 atom type, or * wild card
4 atm4 atom type, or * wild card
5 btype bond type
6 Emax  max. of potential (Kcal mol-1)
7 s*p p: periodicity, s=-1: min. eclipsed, s=1: min staggered
8 source comment, e.g. TAFF5.2, guess, ...

Example: improved *-C.ar-C.ar-C.ar torsion around aromatic bond:

* C.ar C.ar C.ar ar 6.500 -2 A.Widmer


TAFF_VDW: contains parameters for the van der Waals potential. If the first character of a line is '#', the whole line will be treated as comment. If the first character of a line is '#', the whole line will be treated as comment.
 
Field Label Comment
1 atm atom type
2 r radius (Å)
3 eps epsilon (Kcal mol-1)
4 source comment, e.g. TAFF5.2, guess, ...

Example: "guestimated" parameters for B.3

B.3 1.500 0.042 A.Widmer

Parameter assignment rules:

When assigning parameters to the energy terms, Minimax compares atom types TE in the energy term with atom types TP in the parameter definitions. Four situations may occur:
    1. exact match: TE = TP
    2. equivalent match: the "equivalent type" (according to ATOM_DEF) of  TE = TP
    3. wild match: TP = *
    4. mismatch: all other cases
Among the definitions without mismatches, the one with the fewest wild matches will be used in the parameter assignment. If this rule does not unambiguously determine the definition to be used, the ambiguity will be resolved in favor of the definition with the highest number of exact matches. Finally, if there is still ambiguity, the definition which occurs first in the parameter file will take precedence over later definitions. If no definition without mismatches is found, an error message will be issued, and the program will terminate.


Reference:

1. M. Clark, R.D. Cramer III, N. Van Opdenbosch:
Validation of the general purpose Tripos 5.2 force-field,
J.Comput.Chem. 10, 982-1012, 1989.



A.Widmer, NIBR/CPC/CSG-SB