[gmx-users] No default Ryckaert-Bell. types
Daniele Veclani
danieleveclani at gmail.com
Thu Sep 3 13:19:21 CEST 2015
Dear Naga Rajesh Tummala
I read in the manual the part relating to Ryckaert-Bell. angles.
But I did not understand how to enter the 5 parameters.
Do you tell me where I can find a guide?
Best regard
2015-09-02 18:02 GMT+02:00 Naga Rajesh Tummala <nagarajesh at gatech.edu>:
> In the dihedrals section, similar to the bonds and angles section, the
> parameters are followed after the dihedral type..
>
> 2 1 3 4 3 v0 v1 v2 v3 v4 v5 for RB type
>
>
>
> On Wed, Sep 2, 2015 at 11:48 AM, Daniele Veclani <danieleveclani at gmail.com
> >
> wrote:
>
> > Thank you for your answer.
> >
> > how can I put these parameters in the .top file?
> >
> > Best regard.
> >
> >
> >
> > 2015-09-02 17:34 GMT+02:00 Naga Rajesh Tummala <nagarajesh at gatech.edu>:
> >
> > > 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
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
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> > > > posting!
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> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > >
> > >
> > >
> > > --
> > > Naga Rajesh Tummala
> > > Research Scientist
> > > School of Chemistry and Biochemistry
> > > Georgia Institute of Technology
> > > email: nagarajesh at gatech.edu
> > > ph: 405-200-7208
> > > --
> > > Gromacs Users mailing list
> > >
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> > > posting!
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> > >
> > --
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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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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