[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
More information about the gromacs.org_gmx-users
mailing list