[gmx-users] OPLSAA.ff

[Hari Pandey]

Dear Gromacs users,

I am a new user and I have some questions
 I confused about indexing.  in atomtypes.atp  clearly  we can know the index is for what kind of atom but  in ffbondedtype.itp there is different kind of the indexing  so I confused how do i pathch the force field . 
Some are obvious (OH, is oxygen bonden to hydrogen and HO is a hydrogen
bonded to oxygen)
but definitively I dont know what type of bond makes the carbon atoms like
C_2, C_3 or C *
Can somebody help me what represents in ffbonded.atp.
for example : opls_083  means S in RSR , opls_091  means CH2 in RCH2SR   but what type of atoms are C*, C_2, C_3 ,  CT, CM, CS, LP, CT_2, CT_3,  CW, NB etc.  


could you please provide me idea or list for that if somebody have.
Thanks


In Oplsaa.ff the indexing is  as follows :

atomtypes.atp


opls_079    1.00800  ; H(O) ALCOHOLS     JPC,90,1276 (1986)
 opls_080   15.03500  ; CH3 IN METHANOL   JPC,90,1276 (1986)
 opls_081   14.02700  ; CH2 IN ETHANOL    JPC,90,1276 (1986)
 opls_082   32.06000  ; S   IN H2S        JPC,90,6379 (1986)
 opls_083   32.06000  ; S   IN RSH        JPC,90,6379 (1986)
 opls_084   32.06000  ; S   IN RSR        JPC,90,6379 (1986)
 opls_085   32.06000  ; S   IN RSSR       JPC,90,6379 (1986)
 opls_086    1.00800  ; H   IN H2S        JPC,90,6379 (1986)
 opls_087    1.00800  ; H(S) IN RSH       JPC,90,6379 (1986)
 opls_088   15.03500  ; CH3 IN CH3SH      JPC,90,6379 (1986)
 opls_089   14.02700  ; CH2 IN CH3CH2SH   JPC,90,6379 (1986)
 opls_090   15.03500  ; CH3 IN CH3SR      JPC,90,6379 (1986)
 opls_091   14.02700  ; CH2 IN RCH2SR     JPC,90,6379 (1986

The ffbonded.itp is as follows ; Some esoteric OPLS atomtypes are not freely available (or depreciated).
; Interaction types involving these have been commented out. [ bondtypes ]
; i    j  func       b0          kb OW    HW      1    0.09572   502080.0   ; For TIP4F Water - wlj 1/98 OW    LP      1    0.01750   753120.0   ;          -idem- C*    HC      1    0.10800   284512.0   ; C     C3      1    0.15220   265265.6   ; END C_2   C3      1    0.15220   265265.6   ; END C_3   C3      1    0.15220   265265.6   ; END C     CA      1    0.14900   334720.0   ; wlj 8/97 C_2   CA      1    0.14900   334720.0   ; wlj 8/97 C_3   CA      1    0.14900   334720.0   ; wlj 8/97 C     CB      1    0.14190   374049.6   ; GUA C_2   CB      1    0.14190   374049.6   ; GUA C_3   CB      1    0.14190   374049.6   ; GUA C     CM      1    0.14440   343088.0   ; THY C_2   CM      1    0.14440   343088.0   ; THY C_3   CM      1    0.14440   343088.0   ; THY C     CS      1    0.14900   334720.0   ; C_2   CS      1    0.14900   334720.0   ; C_3   CS      1    0.14900   334720.0   ; C     CT      1    0.15220   265265.6   ; C_2   CT      1    0.15220  
 265265.6   ; C_3   CT      1    0.15220   265265.6   ; C     CT_2    1    0.15220   265265.6   ; AA Calpha C_3   CT_2    1    0.15220   265265.6   ; AA C-term NO    ON      1    0.12250   460240.0   ; wlj nitro CS    CW      1    0.13670   456892.8   ; wj/nm CS    CS      1    0.14240   392459.2   ; -idem- CS    CB      1    0.14240   392459.2   ; -idem- CS    HA      1    0.10800   307105.6   ; -idem- CU    NB      1    0.13200   343088.0   ; -idem- CU    CA      1    0.14210   392459.2   ; -idem- CU    HA      1    0.10800   307105.6   ; -idem- NA    NB      1    0.13490   334720.0   ; -idem- OS    NB      1    0.13990   386601.6   ; -idem- OS    CR      1    0.13570   386601.6   ; -idem- C3    C3      1    0.15260   217568.0   ; Ethane C!    C!      1    0.14600   322168.0   ; wlj C!    CS      1    0.14600   322168.0   ; wlj