[gmx-users] No default Ryckaert-Bell. types
Naga Rajesh Tummala
nagarajesh at gatech.edu
Wed Sep 2 17:34:40 CEST 2015
The parameters for the RB dihedral in line 227 are not described in the
opls forcefield. Either you can provide the parameters in your top file or
include the dihedral paramters in the opls forcefield files tht comes with
gromacs.
On Wed, Sep 2, 2015 at 11:28 AM, Daniele Veclani <danieleveclani at gmail.com>
wrote:
> Dear users.
>
>
> I'm trying to build the file .top for a molecule with opls FF.
>
> To do this I used MKTOP but when I run grompp I get this error:
>
> "ERROR 23 [file nor.top, line 227]:
> No default Ryckaert-Bell. types"
>
> This is my file .top:
>
> [ moleculetype ]
> ; Name nrexcl
> MOL 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> 1 opls_268 1 MOL O1 1 -0.61100 15.9994
> 2 opls_270 1 MOL H1 1 0.44100 1.008
> 3 opls_267 1 MOL C1 1 0.81100 12.011
> 4 opls_269 1 MOL O2 1 -0.54900 15.9994
> 5 opls_141 1 MOL C2 2 -0.52100 12.011
> 6 opls_145 1 MOL C3 3 0.07300 12.011
> 7 opls_140 1 MOL H2 3 0.14200 1.008
> 8 opls_280 1 MOL C4 4 0.62500 12.011
> 9 opls_281 1 MOL O3 4 -578.00000 15.9994
> 10 opls_145 1 MOL C5 5 -0.12600 12.011
> 11 opls_145B 1 MOL C6 6 0.13300 12.011
> 12 opls_145 1 MOL C7 7 -0.26700 12.011
> 13 opls_146 1 MOL H3 7 0.19900 1.008
> 14 opls_718 1 MOL C8 8 0.27000 12.011
> 15 opls_719 1 MOL F1 8 -0.18000 18.9984
> 16 opls_145 1 MOL C9 9 0.03900 12.011
> 17 opls_145 1 MOL C10 10 -0.24200 12.011
> 18 opls_146 1 MOL H4 10 0.15800 1.008
> 19 opls_902 1 MOL N1 9 -0.11600 14.0067
> 20 opls_908 1 MOL C11 11 -0.12000 12.011
> 21 opls_140 1 MOL H5 11 0.09300 1.008
> 22 opls_140 1 MOL H6 11 0.07400 1.008
> 23 opls_907 1 MOL C12 12 0.11300 12.011
> 24 opls_140 1 MOL H7 12 0.07600 1.008
> 25 opls_140 1 MOL H8 12 0.05500 1.008
> 26 opls_908 1 MOL C13 13 -0.12400 12.011
> 27 opls_140 1 MOL H9 13 0.07300 1.008
> 28 opls_140 1 MOL H10 13 0.07700 1.008
> 29 opls_907 1 MOL C14 14 0.10200 12.011
> 30 opls_140 1 MOL H11 14 0.08500 1.008
> 31 opls_140 1 MOL H12 14 0.05300 1.008
> 32 opls_901 1 MOL N2 12 -0.71000 14.0067
> 33 opls_910 1 MOL H13 12 0.35700 1.008
> 34 opls_902 1 MOL N3 3 -0.11200 14.0067
> 35 opls_908 1 MOL C15 15 0.19100 12.011
> 36 opls_140 1 MOL H14 15 0.03700 1.008
> 37 opls_140 1 MOL H15 15 0.00000 1.008
> 38 opls_135 1 MOL C16 16 -0.26000 12.011
> 39 opls_140 1 MOL H16 16 0.08900 1.008
> 40 opls_140 1 MOL H17 16 0.08000 1.008
> 41 opls_140 1 MOL H18 16 0.07500 1.008
>
>
>
>
> [ bonds ]
> 1 2 1 0.099 462750.4
> 1 3 1 0.133 376560.0
> 3 4 1 0.121 476976.0
> 3 5 1 0.150 343088.0
> 5 6 1 0.137 357313.6
> 5 8 1 0.145 343088.0
> 6 7 1 0.108 284512.0
> 6 34 1 0.135 402500.8
> 8 9 1 0.125 476976.0
> 8 10 1 0.147 334720.0
> 10 11 1 0.141 392459.2
> 10 12 1 0.141 392459.2
> 11 17 1 0.141 392459.2
> 11 34 1 0.140 200000.0
> 12 13 1 0.108 307105.6
> 12 14 1 0.136 392459.2
> 14 15 1 0.135 351456.0
> 14 16 1 0.142 392459.2
> 16 17 1 0.140 392459.2
> 16 19 1 0.140 402500.8
> 17 18 1 0.108 307105.6
> 19 20 1 0.148 319657.6
> 19 26 1 0.146 319657.6
> 20 21 1 0.109 284512.0
> 20 22 1 0.110 284512.0
> 20 23 1 0.153 224262.4
> 23 24 1 0.109 284512.0
> 23 25 1 0.109 284512.0
> 23 32 1 0.146 319657.6
> 26 27 1 0.109 284512.0
> 26 28 1 0.111 284512.0
> 26 29 1 0.154 224262.4
> 29 30 1 0.110 284512.0
> 29 31 1 0.109 284512.0
> 29 32 1 0.146 319657.6
> 32 33 1 0.102 363171.2
> 34 35 1 0.147 319657.6
> 35 36 1 0.109 284512.0
> 35 37 1 0.109 284512.0
> 35 38 1 0.153 224262.4
> 38 39 1 0.109 284512.0
> 38 40 1 0.109 284512.0
> 38 41 1 0.109 284512.0
>
>
> [ angles ]
> 1 3 4 1 122.613 669.440
> 1 3 5 1 115.207 585.760
> 2 1 3 1 108.493 292.880
> 3 5 6 1 117.303 585.760
> 3 5 8 1 122.815 585.760
> 4 3 5 1 122.180 669.440
> 5 6 7 1 118.516 418.400
> 5 6 34 1 124.720 669.440
> 5 8 9 1 123.231 669.440
> 5 8 10 1 115.012 585.760
> 6 5 8 1 119.879 585.760
> 6 34 11 1 119.618 669.440
> 6 34 35 1 118.344 418.400
> 7 6 34 1 116.763 669.440
> 8 10 11 1 121.987 585.760
> 8 10 12 1 119.361 711.280
> 9 8 10 1 121.756 669.440
> 10 11 17 1 119.731 527.184
> 10 11 34 1 118.777 669.440
> 10 12 13 1 118.733 292.880
> 10 12 14 1 120.570 527.184
> 11 10 12 1 118.650 527.184
> 11 17 16 1 121.908 527.184
> 11 17 18 1 119.847 292.880
> 11 34 35 1 121.996 669.440
> 12 14 15 1 118.664 669.440
> 12 14 16 1 122.613 527.184
> 13 12 14 1 120.674 292.880
> 14 16 17 1 116.514 527.184
> 14 16 19 1 120.514 585.760
> 15 14 16 1 118.701 669.440
> 16 17 18 1 118.239 292.880
> 16 19 20 1 118.014 418.400
> 16 19 26 1 118.505 418.400
> 17 16 19 1 122.909 585.760
> 17 11 34 1 121.479 669.440
> 19 20 21 1 109.602 292.880
> 19 20 22 1 109.264 292.880
> 19 20 23 1 110.216 470.281
> 19 26 27 1 108.879 292.880
> 19 26 28 1 111.356 292.880
> 19 26 29 1 109.952 470.281
> 20 19 26 1 112.364 433.462
> 20 23 24 1 108.725 313.800
> 20 23 25 1 109.654 313.800
> 20 23 32 1 113.538 470.281
> 21 20 22 1 107.958 276.144
> 21 20 23 1 110.212 313.800
> 22 20 23 1 109.548 313.800
> 23 32 29 1 110.898 433.462
> 23 32 33 1 109.659 292.880
> 24 23 25 1 107.559 276.144
> 24 23 32 1 108.141 292.880
> 25 23 32 1 109.046 292.880
> 26 29 30 1 108.376 313.800
> 26 29 31 1 109.441 313.800
> 26 29 32 1 114.130 470.281
> 27 26 28 1 107.895 276.144
> 27 26 29 1 109.290 313.800
> 28 26 29 1 109.422 313.800
> 29 32 33 1 109.749 292.880
> 30 29 31 1 107.504 276.144
> 30 29 32 1 107.978 292.880
> 31 29 32 1 109.197 292.880
> 34 35 36 1 106.499 292.880
> 34 35 37 1 108.568 292.880
> 34 35 38 1 113.397 470.281
> 35 38 39 1 110.715 313.800
> 35 38 40 1 111.818 313.800
> 35 38 41 1 109.750 313.800
> 36 35 37 1 106.377 276.144
> 36 35 38 1 110.144 313.800
> 37 35 38 1 111.500 313.800
> 39 38 40 1 108.100 276.144
> 39 38 41 1 108.087 276.144
> 40 38 41 1 108.258 276.144
>
>
> [ dihedrals ]
> 2 1 3 4 3
> 2 1 3 5 3
> 1 3 5 6 3
> 4 3 5 6 3
> 1 3 5 8 3
> 4 3 5 8 3
> 3 5 6 7 3
> 8 5 6 7 3
> 3 5 6 34 3
> 8 5 6 34 3
> 3 5 8 9 3
> 6 5 8 9 3
> 3 5 8 10 3
> 6 5 8 10 3
> 5 6 34 11 3
> 7 6 34 11 3
> 5 6 34 35 3
> 7 6 34 35 3
> 5 8 10 11 3
> 9 8 10 11 3
> 5 8 10 12 3
> 9 8 10 12 3
> 8 10 11 17 3
> 12 10 11 17 3
> 8 10 11 34 3
> 12 10 11 34 3
> 8 10 12 13 3
> 11 10 12 13 3
> 8 10 12 14 3
> 11 10 12 14 3
> 10 11 17 16 3
> 34 11 17 16 3
> 10 11 17 18 3
> 34 11 17 18 3
> 10 11 34 6 3
> 17 11 34 6 3
> 10 11 34 35 3
> 17 11 34 35 3
> 10 12 14 15 3
> 13 12 14 15 3
> 10 12 14 16 3
> 13 12 14 16 3
> 12 14 16 17 3
> 15 14 16 17 3
> 12 14 16 19 3
> 15 14 16 19 3
> 14 16 17 11 3
> 19 16 17 11 3
> 14 16 17 18 3
> 19 16 17 18 3
> 14 16 19 20 3
> 17 16 19 20 3
> 14 16 19 26 3
> 17 16 19 26 3
> 16 19 20 21 3
> 26 19 20 21 3
> 16 19 20 22 3
> 26 19 20 22 3
> 16 19 20 23 3
> 26 19 20 23 3
> 16 19 26 27 3
> 20 19 26 27 3
> 16 19 26 28 3
> 20 19 26 28 3
> 16 19 26 29 3
> 20 19 26 29 3
> 19 20 23 24 3
> 21 20 23 24 3
> 22 20 23 24 3
> 19 20 23 25 3
> 21 20 23 25 3
> 22 20 23 25 3
> 19 20 23 32 3
> 21 20 23 32 3
> 22 20 23 32 3
> 20 23 32 29 3
> 24 23 32 29 3
> 25 23 32 29 3
> 20 23 32 33 3
> 24 23 32 33 3
> 25 23 32 33 3
> 19 26 29 30 3
> 27 26 29 30 3
> 28 26 29 30 3
> 19 26 29 31 3
> 27 26 29 31 3
> 28 26 29 31 3
> 19 26 29 32 3
> 27 26 29 32 3
> 28 26 29 32 3
> 26 29 32 23 3
> 30 29 32 23 3
> 31 29 32 23 3
> 26 29 32 33 3
> 30 29 32 33 3
> 31 29 32 33 3
> 6 34 35 36 3
> 11 34 35 36 3
> 6 34 35 37 3
> 11 34 35 37 3
> 6 34 35 38 3
> 11 34 35 38 3
> 34 35 38 39 3
> 36 35 38 39 3
> 37 35 38 39 3
> 34 35 38 40 3
> 36 35 38 40 3
> 37 35 38 40 3
> 34 35 38 41 3
> 36 35 38 41 3
> 37 35 38 41 3
>
>
> [ dihedrals ]
> 1 4 3 0 1 improper_O_C_X_Y
> 3 6 5 8 1 improper_Z_CM_X_Y
> 5 7 6 34 1 improper_Z_CA_X_Y
> 5 10 8 9 1 improper_O_C_X_Y
> 8 11 10 12 1 improper_Z_CA_X_Y
> 10 13 12 14 1 improper_Z_CA_X_Y
> 12 15 14 16 1 improper_Z_CA_X_Y
> 14 17 16 19 1 improper_Z_CA_X_Y
> 16 11 17 18 1 improper_Z_CA_X_Y
>
>
> [ pairs ]
> 4 2 1
> 5 2 1
> 6 1 1
> 6 4 1
> 8 1 1
> 8 4 1
> 7 3 1
> 7 8 1
> 34 3 1
> 34 8 1
> 9 3 1
> 9 6 1
> 10 3 1
> 10 6 1
> 11 5 1
> 11 7 1
> 35 5 1
> 35 7 1
> 11 5 1
> 11 9 1
> 12 5 1
> 12 9 1
> 17 8 1
> 17 12 1
> 34 8 1
> 34 12 1
> 13 8 1
> 13 11 1
> 14 8 1
> 14 11 1
> 16 10 1
> 16 34 1
> 18 10 1
> 18 34 1
> 6 10 1
> 6 17 1
> 35 10 1
> 35 17 1
> 15 10 1
> 15 13 1
> 16 10 1
> 16 13 1
> 17 12 1
> 17 15 1
> 19 12 1
> 19 15 1
> 11 14 1
> 11 19 1
> 18 14 1
> 18 19 1
> 20 14 1
> 20 17 1
> 26 14 1
> 26 17 1
> 21 16 1
> 21 26 1
> 22 16 1
> 22 26 1
> 23 16 1
> 23 26 1
> 27 16 1
> 27 20 1
> 28 16 1
> 28 20 1
> 29 16 1
> 29 20 1
> 24 19 1
> 24 21 1
> 24 22 1
> 25 19 1
> 25 21 1
> 25 22 1
> 32 19 1
> 32 21 1
> 32 22 1
> 29 20 1
> 29 24 1
> 29 25 1
> 33 20 1
> 33 24 1
> 33 25 1
> 30 19 1
> 30 27 1
> 30 28 1
> 31 19 1
> 31 27 1
> 31 28 1
> 32 19 1
> 32 27 1
> 32 28 1
> 23 26 1
> 23 30 1
> 23 31 1
> 33 26 1
> 33 30 1
> 33 31 1
> 36 6 1
> 36 11 1
> 37 6 1
> 37 11 1
> 38 6 1
> 38 11 1
> 39 34 1
> 39 36 1
> 39 37 1
> 40 34 1
> 40 36 1
> 40 37 1
> 41 34 1
> 41 36 1
> 41 37 1
>
>
> [ system ]
> ; Name
> nor
>
> [ molecules ]
> ; Compound #mols
> MOL 1
>
>
> Where is the problem?
>
> I use gromacs 5.0.4
> --
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--
Naga Rajesh Tummala
Research Scientist
School of Chemistry and Biochemistry
Georgia Institute of Technology
email: nagarajesh at gatech.edu
ph: 405-200-7208
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