APPENDIX C - TRIPOS atom types

The TRIPOS.tem file is stored in Data directory and it contains the new atom types with more than four character length.

 

#TemplateFF TRIPOS 3.1

; ******************************
; ****  VEGA Template V4.0  ****
; ****  Force Field TRIPOS  ****
; ******************************


; ATDL atom description:
; ~~~~~~~~~~~~~~~~~~~~~~
; Element (2) - Bond order (1) - Ring indicator (1) - Aromatic indicator (1)
;
; The brackets indicates the length in characters of each field.

; Generic elements:                     Bond order:
; ~~~~~~~~~~~~~~~~~                     ~~~~~~~~~~~
; X = Any atom                          0   = Atom not bonded
; # = Heavy atom                        1-6 = Bond order
; $ = Any atom excluding C and H        9   = Any bond order
; @ = Halogen
; - = None

; Ring indicator:                       Aromatic indicator:
; ~~~~~~~~~~~~~~~                       ~~~~~~~~~~~~~~~~~~~
; 0     = Don't check ring              0 = Don't check
; 2     = Not inside a ring             1 = Aromatic
; 3...7 = From 3 to 7 member ring
; 9     = Generic ring

; Logical operators:
; ~~~~~~~~~~~~~~~~~~
; to use the logical operators AND, OR and NOT (&, | and !), you must
; place the expression between square brackets at the specified position:
;
; Examples:
; [C- |  N-]900  -> the element can be carbon or nitrogen
; [X- & !Cl]900  -> all elements but not chlorine
; C-[4 | 3]00    -> sp3 or sp2 carbon
; C-4[9 & 9]0    -> sp3 carbon in a double condensed ring
; C-3[6 | 5][!1] -> sp2 carbon in 5 or 6 member ring not aromatic

; Atom types:
; ~~~~~~~~~~~
; each not blank and not commented line (; is the remark indicator) must
; include at least the atom type name (max. 8 characters) and the ATDL
; description. Optionally, you can specify the bonded atoms placing them
; between round brackets.


; Type    Atm    Bonded atoms
; ========================================================================

  H.t3p  H-100 (O-200 (H-100 H-100))
; H.spc  H-100 (O-200 (H-100 H-100))
  H      H-100

  C.3    C-400
  C.ar   C-391
  C.cat  C-300 (N-300 N-300 N-300)
  C.2    C-300
  C.1    C-200

  N.4    N-400
  N.ar   N-391
  N.am   N-300 (C-300 (O-100))
  N.pl3  N-300 (C-300)
  N.3    N-300
  N.ar   N-291
  N.2    N-200
  N.1    N-100

  O.t3p  O-200 (H-100 H-100)
; O.spc  O-200 (H-100 H-100)
  O.3    O-200
  O.ar   O-291
  O.co2  O-100 (C-300 (O-100 O-100))
  O.co2  O-100 (P-400 (O-100 O-100 O-100))
  O.2    O-100

  S.3    S-400 (Lp100 Lp100)
  S.O2   S-400 (O-100 O-100)
  S.O    S-300 (O-100)
  S.3    S-200
; S.ar   S-291
  S.2    S-100

  P.3    P-400

  I      I-100
  I      I-000
  F      F-100
  F      F-000
  Cl     Cl100
  Cl     Cl000
  Br     Br100
  Br     Br000

  Se     Se900
  Si     Si400

  Na     Na900
  K      K-900
  Ca     Ca900
  Mg     Mg900
  Li     Li900
  Al     Al900
  Fe     Fe900
  Mn     Mn900
  Mo     Mo900
  Co.oh  Co900
  Cr.th  Cr300
  Cr.oh  Cr600
  Zn     Zn900
  Sn     Sn900

  Du     Du900
  LP     Lp900

  Hev    #-900
  Any    X-900