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
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.