APPENDIX C - CVFF atom types
The CVFF.tem file is stored in Data directory.
#TemplateFF CVFF 3.0 ; ****************************** ; **** VEGA Template V4.0 **** ; **** Force Field CVFF **** ; ****************************** ; 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 ; ========================================================================; 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 H-100 (C-900) h+ H-100 (N-400) hn H-100 (N-900) h* H-100 (O-200 (H-100 H-100)) ho H-100 (O-900) hp H-100 (P-900) hs H-100 (S-900) dw D-100 (O-200 (D-100 H-100)) dw D-100 (O-200 (D-100 D-100)) d D-100 (X-900) c3h C-430 (C-430 H-100 H-100 #-930) c3m C-430 (C-430 #-930 X-900 X-900) c4h C-440 (H-100 H-100 X-940 X-940) c4m C-440 (X-940 X-940 X-900 X-900) cg C-400 (N-400 (H-100 H-100) C-300 H-100 H-100) cg C-400 (N-300 (H-100) C-300 H-100 H-100) ca C-400 (N-400 C-300 H-100 X-900) ca C-400 (N-300 C-300 H-100 X-900) coh C-400 (O-200 (C-900) O-200 H-100 X-900) co C-400 (O-200 (C-900) O-200 X-900 X-900) c3 C-400 (H-100 H-100 H-100 X-900) c2 C-400 (H-100 H-100 #-900 #-900) c1 C-400 (H-100 #-900 #-900 #-900) cn C-400 (N-400 X-900 X-900 X-900) cn C-400 (N-300 X-900 X-900 X-900) c C-400 (X-900 X-900 X-900 X-900) ci C-351 (N-351 (H-100) N-351 (H-100) X-900) cs C-351 (S-251 X-951 X-900) c5 C-351 (X-951 X-951 X-900) cp C-391 (X-991 X-991 X-900) cr C-300 (N-300 N-300 N-300) cr C-300 (N-200 N-300 N-300) c' C-300 (O-100 N-300 X-900) c- C-300 (O-100 O-100 X-900) c" C-300 (O-100 X-900 X-900) c= C-300 (X-900 X-900 X-900) ct C-200 (X-900 X-900) n4 N-400 (X-900 X-900 X-900 X-900) ni N-351 (C-351 (N-351) C-351 H-100) np N-391 (X-991 X-991) no N-300 (O-100 O-100) n1 N-300 (C-300 (N-300 N-300) C-400 H-100) n2 N-300 (C-300 (N-300 N-900) H-100 H-100) n N-300 (C-300 (O-100) X-900 X-900) n3 N-300 (X-900 X-900 X-900) np N-291 (X-991 X-991) n= N-200 (X-900 X-900) nt N-100 (X-900) o* O-200 (H-100 H-100) oh O-200 (H-100 X-900) o- O-200 (Mg900 C-900) o- O-200 (Zn900 C-900) o O-200 (X-900 X-900) o- O-300 (Mg900 Mg900 C-900) o- O-100 (C-300 (O-100 O-100)) o- O-100 (P-400) o' O-100 (C-300) o' O-100 (N-300 (O-100 O-100)) o' O-100 (S-400) oo O-900 (O-900 Fe900) s S-400 sh S-200 (H-100 C-900) s S-200 (C-900 X-900) s1 S-200 (S-200 X-900) s S-100 p P-900 si Si900 f F-100 (C-900) cl Cl100 (C-900) Cl Cl000 br Br100 (C-900) Br Br000 i I-900 ar Ar000 Na Na000 c+ Ca000 c+ Mg900 cu Cu900 fe Fe900 pt Pt900 Zn Zn900 nu Nu900