[gmx-users] OPLS force field issue

[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. Where should I add these properties? It seems different from gromos where you can add g_a, g_b, and g_d in fbonded.itp.

Thanks,
Ehsan

[ 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