[gmx-users] No default Ryckaert-Bell. types

Daniele Veclani danieleveclani at gmail.com
Wed Sep 2 17:28:29 CEST 2015


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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