[gmx-users] OPLS force field parameters

[Ehsan Sadeghi]

Hi gmx users,

I try to use OPLS force field for my simulation. I added the following residue to the aminoacids.rtp, but when I generate the topol.top file it does not show the the bond stretching, angle bond, dihedrals. 


[ NAF ]
   [ atoms ]
     C1    opls_966   0.3846     1
     C2    opls_966   0.3846     1
     C3    opls_966   0.3846     1
     C4    opls_966   0.3846     1
     F17   opls_972  -0.1923     1
     F18   opls_972  -0.1923     1
     F19   opls_972  -0.1923     1
     F20   opls_972  -0.1923     1
     F21   opls_972  -0.1923     1
     F22   opls_972  -0.1923     1
     F23   opls_972  -0.1923     1
     F24   opls_972  -0.1923     1
     C5    opls_966   0.3846     1
     C6    opls_966   0.3846     1
     C7    opls_966   0.3846     1
     C8    opls_966   0.3846     1
     F25   opls_972  -0.1923     1
     F26   opls_972  -0.1923     1
     F27   opls_972  -0.1923     1
     F28   opls_972  -0.1923     1
     F29   opls_972  -0.1923     1
     F30   opls_972  -0.1923     1
     F31   opls_972  -0.1923     1
     F32   opls_972  -0.1923     1
     C9    opls_966   0.3846     1
     C10   opls_966   0.3846     1
     C11   opls_966   0.3846     1
     C12   opls_966   0.3846     1
     F33   opls_972  -0.1923     1
     F34   opls_972  -0.1923     1
     F35   opls_972  -0.1923     1
     F36   opls_972  -0.1923     1
     F37   opls_972  -0.1923     1
     F38   opls_972  -0.1923     1
     F39   opls_972  -0.1923     1
     F40   opls_972  -0.1923     1
     C13   opls_966   0.3846     1
     C14   opls_966   0.3846     1
     C15   opls_967   0.3218     1
     C16   opls_966   0.3846     1
     F41   opls_972  -0.1923     1
     F42   opls_972  -0.1923     1
     F43   opls_972  -0.1923     1
     F44   opls_972  -0.1923     1
     F45   opls_973  -0.1641     1
     F46   opls_972  -0.1923     1
     F47   opls_972  -0.1923     1
     C48   opls_968   0.3228     1
     O49   opls_980  -0.2742     1
     C50   opls_969   0.401      1
     O51   opls_981  -0.2604     1
     C52   opls_967   0.3218     1
     C53   opls_971   0.3216     1
     F55   opls_974  -0.1637     1
     F56   opls_974  -0.1637     1
     F57   opls_975  -0.1932     1
     C58   opls_970   0.4947     1
     F59   opls_977  -0.1662     1
     F60   opls_977  -0.1662     1
     F61   opls_978  -0.3278     1
     F62   opls_978  -0.3278     1
     F66   opls_976  -0.1649     1
     F67   opls_976  -0.1649     1
     F68   opls_976  -0.1649     1
     S54   opls_979   1.4124     1
     O63   opls_982  -0.632      1
     O64   opls_982  -0.632      1
     O65   opls_982  -0.632      1
     [ bonds ]
      C1     C2
      C2     C3
      C3     C4
      C4     C5
      C5     C6
      C6     C7
      C7     C8
      C8     C9
      C9     C10
      C10    C11
      C11    C12
      C12    C13
      C13    C14
      C14    C15
      C15    C16
      F17    C1
      F18    C1
      F19    C2
      F20    C2
      F21    C3
      F22    C3
      F23    C4
      F24    C4
      F25    C5
      F26    C5
      F27    C6
      F28    C6
      F29    C7
      F30    C7
      F31    C8
      F32    C8
      F33    C9
      F34    C9
      F35    C10
      F36    C10
      F37    C11
      F38    C11
      F39    C12
      F40    C12
      F41    C13
      F42    C13
      F43    C14
      F44    C14
      F45    C15
      F46    C16
      F47    C16
      C15    O49
      O49    C48
      F55    C48
      F56    C48
      C48    C50
      F57    C50
      C50    C58
      C58    F66
      C58    F67
      C58    F68
      C50    O51
      O51    C52
      C52    F59
      C52    F60
      C52    C53
      C53    F61
      C53    F62
      C53    S54
      S54    O63
      S54    O64
      S54    O65
--------------------------------

I added the bond description in the ffbonded.itp but it does not show in the topol.top file.

In ffbonded.itp we have:

[ 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   ;
  C1    C2       1    0.16020   292880.0   ;
  C2    C3       1    0.16020   292880.0   ;

" I am not sure to put C   C or C1   C2 here; I tried both, neither worked."

[ angletypes ]
;  i    j    k  func       th0       cth
  HW     OW     HW      1   109.500    627.600   ; For TIP4F Water - wj 1/98
  HW     OW     LP      1    54.750    418.400   ; For TIP4F Water - wj 1/98
  OU     U      OU      1   180.000   1255.200   ; J Phys Chem 97, 5685 (1993)
  HC     C*     CW      1   126.800    292.880   ;
  HC     C*     CB      1   126.800    292.880   ;
  HC     CS     CW      1   126.800    292.880   ;

----------------
However, the parameters that we had in topol file are different:

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1
    1     5     1

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
    2     1     5     1
    2     1     6     1
    5     1     6     1
--------------------------------

How gromacs can find c0, c1,c2 and c3 from b0, kb, th0, and cth in the ffbonded.itp?

Kind regards,
Ehsan