[gmx-users] OPLS force field issue

[Justin Lemkul]

On 12/6/13 1:46 PM, Ehsan Sadeghi wrote:
> 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.
>

OPLS atom types have opls_* names and what are called "bonded atom types" (in 
the second column of ffnonbonded.itp).  These atom types are used in 
ffbonded.itp to define bonded interactions.  When grompp is called, parameters 
are read from ffbonded.itp and written into the .tpr file.  If parameters are 
missing for a given combination, a fatal error is triggered.  Of course, one 
should always be able to add the parameters directly in the .rtp, or even the 
.top, if desired.

-Justin

> 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
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================