[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
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > 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
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
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> > posting!
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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
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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