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