No default Improper Dih. types

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GROMACS version:2024.2
GROMACS modification: Yes/No
Here post your question

I was using CGENFF to generate parameters for the small molecules using charmm36 force field. But for my current compound, I am getting error like below:

ERROR 1 [file unl.itp, line 148]:
No default Bond types

ERROR 2 [file unl.itp, line 410]:
No default U-B types

ERROR 3 [file unl.itp, line 411]:
No default U-B types

ERROR 4 [file unl.itp, line 470]:
No default U-B types

ERROR 5 [file unl.itp, line 472]:
No default U-B types

ERROR 6 [file unl.itp, line 473]:
No default U-B types

ERROR 7 [file unl.itp, line 474]:
No default U-B types

ERROR 8 [file unl.itp, line 478]:
No default U-B types

ERROR 9 [file unl.itp, line 479]:
No default U-B types

ERROR 10 [file unl.itp, line 492]:
No default U-B types

ERROR 11 [file unl.itp, line 512]:
No default U-B types

ERROR 12 [file unl.itp, line 573]:
No default Proper Dih. types

ERROR 13 [file unl.itp, line 574]:
No default Proper Dih. types

ERROR 14 [file unl.itp, line 575]:
No default Proper Dih. types

ERROR 15 [file unl.itp, line 576]:
No default Proper Dih. types

ERROR 16 [file unl.itp, line 577]:
No default Proper Dih. types

ERROR 17 [file unl.itp, line 578]:
No default Proper Dih. types

ERROR 18 [file unl.itp, line 579]:
No default Proper Dih. types

ERROR 19 [file unl.itp, line 580]:
No default Proper Dih. types

ERROR 20 [file unl.itp, line 583]:
No default Proper Dih. types

ERROR 21 [file unl.itp, line 584]:
No default Proper Dih. types

ERROR 22 [file unl.itp, line 657]:
No default Proper Dih. types

ERROR 23 [file unl.itp, line 665]:
No default Proper Dih. types

ERROR 24 [file unl.itp, line 667]:
No default Proper Dih. types

ERROR 25 [file unl.itp, line 669]:
No default Proper Dih. types

ERROR 26 [file unl.itp, line 670]:
No default Proper Dih. types

ERROR 27 [file unl.itp, line 671]:
No default Proper Dih. types

ERROR 28 [file unl.itp, line 672]:
No default Proper Dih. types

ERROR 29 [file unl.itp, line 675]:
No default Proper Dih. types

ERROR 30 [file unl.itp, line 676]:
No default Proper Dih. types

ERROR 31 [file unl.itp, line 677]:
No default Proper Dih. types

ERROR 32 [file unl.itp, line 678]:
No default Proper Dih. types

ERROR 33 [file unl.itp, line 681]:
No default Proper Dih. types

ERROR 34 [file unl.itp, line 684]:
No default Proper Dih. types

ERROR 35 [file unl.itp, line 685]:
No default Proper Dih. types

ERROR 36 [file unl.itp, line 686]:
No default Proper Dih. types

ERROR 37 [file unl.itp, line 688]:
No default Proper Dih. types

ERROR 38 [file unl.itp, line 690]:
No default Proper Dih. types

ERROR 39 [file unl.itp, line 691]:
No default Proper Dih. types

ERROR 40 [file unl.itp, line 692]:
No default Proper Dih. types

ERROR 41 [file unl.itp, line 693]:
No default Proper Dih. types

ERROR 42 [file unl.itp, line 694]:
No default Proper Dih. types

ERROR 43 [file unl.itp, line 703]:
No default Proper Dih. types

ERROR 44 [file unl.itp, line 712]:
No default Proper Dih. types

ERROR 45 [file unl.itp, line 713]:
No default Proper Dih. types

ERROR 46 [file unl.itp, line 733]:
No default Proper Dih. types

ERROR 47 [file unl.itp, line 735]:
No default Proper Dih. types

ERROR 48 [file unl.itp, line 737]:
No default Proper Dih. types

ERROR 49 [file unl.itp, line 738]:
No default Proper Dih. types

ERROR 50 [file unl.itp, line 746]:
No default Improper Dih. types

Program: gmx grompp, version 2024.2-Homebrew
Source file: src/gromacs/gmxpreprocess/topio.cpp (line 577)

Fatal error:
Syntax error - File unl.prm, line 2
Last line read:
‘[ bondtypes ]’
Invalid order for directive bondtypes

The ipt and prm files creted by CGENFF is as below:

; Created by cgenff_charmm2gmx.py

[ moleculetype ]
; Name nrexcl
UNL 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 UNL rtp UNL q qsum
1 CG2R61 1 UNL C1 1 -0.002 12.011 ;
2 CG2R61 1 UNL C2 2 -0.109 12.011 ;
3 CG2R61 1 UNL C3 3 -0.109 12.011 ;
4 CG2R61 1 UNL C4 4 -0.002 12.011 ;
5 CG2R61 1 UNL C5 5 -0.109 12.011 ;
6 CG2R61 1 UNL C6 6 -0.109 12.011 ;
7 CG321 1 UNL C7 7 -0.003 12.011 ;
8 OG2D1 1 UNL O1 8 -0.508 15.999 ;
9 CG2O1 1 UNL C8 9 0.518 12.011 ;
10 NG2S1 1 UNL N1 10 -0.513 14.007 ;
11 HGP1 1 UNL H1 11 0.337 1.008 ;
12 CG321 1 UNL C9 12 -0.206 12.011 ;
13 NG2R51 1 UNL N2 13 -0.041 14.007 ;
14 CG2RC0 1 UNL C10 14 0.304 12.011 ;
15 CG2R61 1 UNL C11 15 -0.243 12.011 ;
16 CG2R61 1 UNL C12 16 -0.170 12.011 ;
17 CG2R61 1 UNL C13 17 -0.167 12.011 ;
18 CG2R61 1 UNL C14 18 -0.252 12.011 ;
19 CG2R67 1 UNL C15 19 -0.160 12.011 ;
20 CG2R67 1 UNL C16 20 -0.160 12.011 ;
21 CG2R61 1 UNL C17 21 -0.252 12.011 ;
22 CG2R61 1 UNL C18 22 -0.167 12.011 ;
23 CG2R61 1 UNL C19 23 -0.170 12.011 ;
24 CG2R61 1 UNL C20 24 -0.243 12.011 ;
25 CG2RC0 1 UNL C21 25 0.304 12.011 ;
26 CG321 1 UNL C22 26 -0.007 12.011 ;
27 NG2S1 1 UNL N3 27 -0.416 14.007 ;
28 CG2O1 1 UNL C23 28 0.327 12.011 ;
29 OG2D1 1 UNL O2 29 -0.464 15.999 ;
30 HGP1 1 UNL H2 30 0.313 1.008 ;
31 CG2R61 1 UNL C24 31 -0.173 12.011 ;
32 CG2R61 1 UNL C25 32 -0.272 12.011 ;
33 CG2R61 1 UNL C26 33 -0.425 12.011 ;
34 CG2RC0 1 UNL C27 34 0.362 12.011 ;
35 CG2R53 1 UNL C28 35 0.366 12.011 ;
36 OG2D1 1 UNL O3 36 -0.524 15.999 ;
37 NG2R53 1 UNL N4 37 -0.266 14.007 ;
38 CG3C52 1 UNL C29 38 0.454 12.011 ;
39 CG2RC0 1 UNL C30 39 -0.103 12.011 ;
40 CG2R61 1 UNL C31 40 -0.217 12.011 ;
41 CG311 1 UNL C32 41 0.084 12.011 ;
42 CG321 1 UNL C33 42 -0.149 12.011 ;
43 CG321 1 UNL C34 43 -0.207 12.011 ;
44 CG2O1 1 UNL C35 44 0.521 12.011 ;
45 OG2D1 1 UNL O4 45 -0.490 15.999 ;
46 NG2S1 1 UNL N5 46 -0.465 14.007 ;
47 CG2O1 1 UNL C36 47 0.528 12.011 ;
48 OG2D1 1 UNL O5 48 -0.486 15.999 ;
49 HGP1 1 UNL H3 49 0.345 1.008 ;
50 HGR61 1 UNL H4 50 0.115 1.008 ;
51 HGR61 1 UNL H5 51 0.115 1.008 ;
52 HGR61 1 UNL H6 52 0.115 1.008 ;
53 HGR61 1 UNL H7 53 0.115 1.008 ;
54 HGA2 1 UNL H8 54 0.090 1.008 ;
55 HGA2 1 UNL H9 55 0.090 1.008 ;
56 HGA2 1 UNL H10 56 0.090 1.008 ;
57 HGA2 1 UNL H11 57 0.090 1.008 ;
58 HGR61 1 UNL H12 58 0.194 1.008 ;
59 HGR61 1 UNL H13 59 0.127 1.008 ;
60 HGR61 1 UNL H14 60 0.115 1.008 ;
61 HGR61 1 UNL H15 61 0.275 1.008 ;
62 HGR61 1 UNL H16 62 0.275 1.008 ;
63 HGR61 1 UNL H17 63 0.115 1.008 ;
64 HGR61 1 UNL H18 64 0.127 1.008 ;
65 HGR61 1 UNL H19 65 0.194 1.008 ;
66 HGA2 1 UNL H20 66 0.090 1.008 ;
67 HGA2 1 UNL H21 67 0.090 1.008 ;
68 HGR61 1 UNL H22 68 0.127 1.008 ;
69 HGR61 1 UNL H23 69 0.300 1.008 ;
70 HGA2 1 UNL H24 70 0.090 1.008 ;
71 HGA2 1 UNL H25 71 0.090 1.008 ;
72 HGR61 1 UNL H26 72 0.117 1.008 ;
73 HGA1 1 UNL H27 73 0.090 1.008 ;
74 HGA2 1 UNL H28 74 0.090 1.008 ;
75 HGA2 1 UNL H29 75 0.090 1.008 ;
76 HGA2 1 UNL H30 76 0.090 1.008 ;
77 HGA2 1 UNL H31 77 0.090 1.008 ;

[ bonds ]
; ai aj funct c0 c1 c2 c3
1 7 1
1 2 1
1 6 1
2 3 1
2 50 1
3 4 1
3 51 1
4 5 1
4 26 1
5 6 1
5 52 1
6 53 1
7 10 1
7 54 1
7 55 1
8 9 1
9 12 1
9 10 1
10 11 1
12 13 1
12 56 1
12 57 1
13 14 1
13 25 1
14 15 1
14 19 1
15 16 1
15 58 1
16 17 1
16 59 1
17 18 1
17 60 1
18 19 1
18 61 1
19 20 1
20 21 1
20 25 1
21 22 1
21 62 1
22 23 1
22 63 1
23 24 1
23 64 1
24 25 1
24 65 1
26 27 1
26 66 1
26 67 1
27 28 1
27 30 1
28 29 1
28 31 1
31 32 1
31 40 1
32 33 1
32 68 1
33 34 1
33 69 1
34 35 1
34 39 1
35 36 1
35 37 1
37 38 1
37 41 1
38 39 1
38 70 1
38 71 1
39 40 1
40 72 1
41 42 1
41 47 1
41 73 1
42 43 1
42 74 1
42 75 1
43 44 1
43 76 1
43 77 1
44 45 1
44 46 1
46 47 1
46 49 1
47 48 1

[ pairs ]
; ai aj funct c0 c1 c2 c3
1 4 1
1 51 1
1 52 1
1 9 1
1 11 1
2 10 1
2 54 1
2 55 1
2 5 1
2 53 1
2 26 1
3 7 1
3 6 1
3 52 1
3 27 1
3 66 1
3 67 1
4 50 1
4 53 1
4 28 1
4 30 1
5 7 1
5 51 1
5 27 1
5 66 1
5 67 1
6 10 1
6 54 1
6 55 1
6 50 1
6 26 1
7 50 1
7 53 1
7 8 1
7 12 1
8 13 1
8 56 1
8 57 1
8 11 1
9 54 1
9 55 1
9 14 1
9 25 1
10 13 1
10 56 1
10 57 1
11 54 1
11 55 1
11 12 1
12 15 1
12 19 1
12 20 1
12 24 1
13 16 1
13 58 1
13 18 1
13 21 1
13 23 1
13 65 1
14 56 1
14 57 1
14 24 1
14 17 1
14 59 1
14 61 1
14 21 1
15 25 1
15 18 1
15 20 1
15 60 1
16 19 1
16 61 1
17 58 1
17 20 1
18 59 1
18 21 1
18 25 1
19 58 1
19 60 1
19 22 1
19 62 1
19 24 1
20 61 1
20 23 1
20 63 1
20 65 1
21 24 1
21 64 1
22 25 1
22 65 1
23 62 1
24 63 1
25 56 1
25 57 1
25 62 1
25 64 1
26 51 1
26 52 1
26 29 1
26 31 1
27 32 1
27 40 1
28 66 1
28 67 1
28 33 1
28 68 1
28 39 1
28 72 1
29 30 1
29 32 1
29 40 1
30 66 1
30 67 1
30 31 1
31 34 1
31 69 1
31 38 1
32 39 1
32 72 1
32 35 1
33 40 1
33 36 1
33 37 1
33 38 1
34 68 1
34 41 1
34 70 1
34 71 1
34 72 1
35 69 1
35 40 1
35 70 1
35 71 1
35 42 1
35 47 1
35 73 1
36 39 1
36 38 1
36 41 1
37 40 1
37 43 1
37 74 1
37 75 1
37 46 1
37 48 1
38 42 1
38 47 1
38 73 1
38 72 1
39 69 1
39 41 1
40 68 1
40 70 1
40 71 1
41 70 1
41 71 1
41 44 1
41 76 1
41 77 1
41 49 1
42 46 1
42 48 1
42 45 1
43 47 1
43 73 1
43 49 1
44 74 1
44 75 1
44 48 1
45 76 1
45 77 1
45 47 1
45 49 1
46 73 1
46 76 1
46 77 1
47 74 1
47 75 1
48 73 1
48 49 1
50 51 1
52 53 1
58 59 1
59 60 1
60 61 1
62 63 1
63 64 1
64 65 1
68 69 1
73 74 1
73 75 1
74 76 1
74 77 1
75 76 1
75 77 1

[ angles ]
; ai aj ak funct c0 c1 c2 c3
7 1 2 5
7 1 6 5
2 1 6 5
1 2 3 5
1 2 50 5
3 2 50 5
2 3 4 5
2 3 51 5
4 3 51 5
3 4 5 5
3 4 26 5
5 4 26 5
4 5 6 5
4 5 52 5
6 5 52 5
1 6 5 5
1 6 53 5
5 6 53 5
1 7 10 5
1 7 54 5
1 7 55 5
10 7 54 5
10 7 55 5
54 7 55 5
8 9 12 5
8 9 10 5
12 9 10 5
7 10 9 5
7 10 11 5
9 10 11 5
9 12 13 5
9 12 56 5
9 12 57 5
13 12 56 5
13 12 57 5
56 12 57 5
12 13 14 5
12 13 25 5
14 13 25 5
13 14 15 5
13 14 19 5
15 14 19 5
14 15 16 5
14 15 58 5
16 15 58 5
15 16 17 5
15 16 59 5
17 16 59 5
16 17 18 5
16 17 60 5
18 17 60 5
17 18 19 5
17 18 61 5
19 18 61 5
14 19 18 5
14 19 20 5
18 19 20 5
19 20 21 5
19 20 25 5
21 20 25 5
20 21 22 5
20 21 62 5
22 21 62 5
21 22 23 5
21 22 63 5
23 22 63 5
22 23 24 5
22 23 64 5
24 23 64 5
23 24 25 5
23 24 65 5
25 24 65 5
13 25 20 5
13 25 24 5
20 25 24 5
4 26 27 5
4 26 66 5
4 26 67 5
27 26 66 5
27 26 67 5
66 26 67 5
26 27 28 5
26 27 30 5
28 27 30 5
27 28 29 5
27 28 31 5
29 28 31 5
28 31 32 5
28 31 40 5
32 31 40 5
31 32 33 5
31 32 68 5
33 32 68 5
32 33 34 5
32 33 69 5
34 33 69 5
33 34 35 5
33 34 39 5
35 34 39 5
34 35 36 5
34 35 37 5
36 35 37 5
35 37 38 5
35 37 41 5
38 37 41 5
37 38 39 5
37 38 70 5
37 38 71 5
39 38 70 5
39 38 71 5
70 38 71 5
34 39 38 5
34 39 40 5
38 39 40 5
31 40 39 5
31 40 72 5
39 40 72 5
37 41 42 5
37 41 47 5
37 41 73 5
42 41 47 5
42 41 73 5
47 41 73 5
41 42 43 5
41 42 74 5
41 42 75 5
43 42 74 5
43 42 75 5
74 42 75 5
42 43 44 5
42 43 76 5
42 43 77 5
44 43 76 5
44 43 77 5
76 43 77 5
43 44 45 5
43 44 46 5
45 44 46 5
44 46 47 5
44 46 49 5
47 46 49 5
41 47 46 5
41 47 48 5
46 47 48 5

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
2 1 7 10 9
2 1 7 54 9
2 1 7 55 9
6 1 7 10 9
6 1 7 54 9
6 1 7 55 9
7 1 2 3 9
7 1 2 50 9
6 1 2 3 9
6 1 2 50 9
7 1 6 5 9
7 1 6 53 9
2 1 6 5 9
2 1 6 53 9
1 2 3 4 9
1 2 3 51 9
50 2 3 4 9
50 2 3 51 9
2 3 4 5 9
2 3 4 26 9
51 3 4 5 9
51 3 4 26 9
3 4 5 6 9
3 4 5 52 9
26 4 5 6 9
26 4 5 52 9
3 4 26 27 9
3 4 26 66 9
3 4 26 67 9
5 4 26 27 9
5 4 26 66 9
5 4 26 67 9
4 5 6 1 9
4 5 6 53 9
52 5 6 1 9
52 5 6 53 9
1 7 10 9 9
1 7 10 11 9
54 7 10 9 9
54 7 10 11 9
55 7 10 9 9
55 7 10 11 9
8 9 12 13 9
8 9 12 56 9
8 9 12 57 9
10 9 12 13 9
10 9 12 56 9
10 9 12 57 9
8 9 10 7 9
8 9 10 11 9
12 9 10 7 9
12 9 10 11 9
9 12 13 14 9
9 12 13 25 9
56 12 13 14 9
56 12 13 25 9
57 12 13 14 9
57 12 13 25 9
12 13 14 15 9
12 13 14 19 9
25 13 14 15 9
25 13 14 19 9
12 13 25 20 9
12 13 25 24 9
14 13 25 20 9
14 13 25 24 9
13 14 15 16 9
13 14 15 58 9
19 14 15 16 9
19 14 15 58 9
13 14 19 18 9
13 14 19 20 9
15 14 19 18 9
15 14 19 20 9
14 15 16 17 9
14 15 16 59 9
58 15 16 17 9
58 15 16 59 9
15 16 17 18 9
15 16 17 60 9
59 16 17 18 9
59 16 17 60 9
16 17 18 19 9
16 17 18 61 9
60 17 18 19 9
60 17 18 61 9
17 18 19 14 9
17 18 19 20 9
61 18 19 14 9
61 18 19 20 9
14 19 20 21 9
14 19 20 25 9
18 19 20 21 9
18 19 20 25 9
19 20 21 22 9
19 20 21 62 9
25 20 21 22 9
25 20 21 62 9
19 20 25 13 9
19 20 25 24 9
21 20 25 13 9
21 20 25 24 9
20 21 22 23 9
20 21 22 63 9
62 21 22 23 9
62 21 22 63 9
21 22 23 24 9
21 22 23 64 9
63 22 23 24 9
63 22 23 64 9
22 23 24 25 9
22 23 24 65 9
64 23 24 25 9
64 23 24 65 9
23 24 25 13 9
23 24 25 20 9
65 24 25 13 9
65 24 25 20 9
4 26 27 28 9
4 26 27 30 9
66 26 27 28 9
66 26 27 30 9
67 26 27 28 9
67 26 27 30 9
26 27 28 29 9
26 27 28 31 9
30 27 28 29 9
30 27 28 31 9
27 28 31 32 9
27 28 31 40 9
29 28 31 32 9
29 28 31 40 9
28 31 32 33 9
28 31 32 68 9
40 31 32 33 9
40 31 32 68 9
28 31 40 39 9
28 31 40 72 9
32 31 40 39 9
32 31 40 72 9
31 32 33 34 9
31 32 33 69 9
68 32 33 34 9
68 32 33 69 9
32 33 34 35 9
32 33 34 39 9
69 33 34 35 9
69 33 34 39 9
33 34 35 36 9
33 34 35 37 9
39 34 35 36 9
39 34 35 37 9
33 34 39 38 9
33 34 39 40 9
35 34 39 38 9
35 34 39 40 9
34 35 37 38 9
34 35 37 41 9
36 35 37 38 9
36 35 37 41 9
35 37 38 39 9
35 37 38 70 9
35 37 38 71 9
41 37 38 39 9
41 37 38 70 9
41 37 38 71 9
35 37 41 42 9
35 37 41 47 9
35 37 41 73 9
38 37 41 42 9
38 37 41 47 9
38 37 41 73 9
37 38 39 34 9
37 38 39 40 9
70 38 39 34 9
70 38 39 40 9
71 38 39 34 9
71 38 39 40 9
34 39 40 31 9
34 39 40 72 9
38 39 40 31 9
38 39 40 72 9
37 41 42 43 9
37 41 42 74 9
37 41 42 75 9
47 41 42 43 9
47 41 42 74 9
47 41 42 75 9
73 41 42 43 9
73 41 42 74 9
73 41 42 75 9
37 41 47 46 9
37 41 47 48 9
42 41 47 46 9
42 41 47 48 9
73 41 47 46 9
73 41 47 48 9
41 42 43 44 9
41 42 43 76 9
41 42 43 77 9
74 42 43 44 9
74 42 43 76 9
74 42 43 77 9
75 42 43 44 9
75 42 43 76 9
75 42 43 77 9
42 43 44 45 9
42 43 44 46 9
76 43 44 45 9
76 43 44 46 9
77 43 44 45 9
77 43 44 46 9
43 44 46 47 9
43 44 46 49 9
45 44 46 47 9
45 44 46 49 9
44 46 47 41 9
44 46 47 48 9
49 46 47 41 9
49 46 47 48 9

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
9 12 10 8 2
28 31 27 29 2
35 34 37 36 2
44 43 46 45 2
47 41 46 48 2

…

[ bondtypes ]
; i j func b0 kb
CG2R53 CG2RC0 1 0.14200000 301248.00

[ angletypes ]
; i j k func theta0 ktheta ub0 kub
CG2RC0 CG2R53 NG2R53 5 108.500000 460.240000 0.00000000 0.00
CG2RC0 CG2R53 OG2D1 5 127.500000 508.774400 0.00000000 0.00
CG2R53 CG2RC0 CG2R61 5 134.100000 502.080000 0.00000000 0.00
CG2R53 CG2RC0 CG2RC0 5 105.900000 753.120000 0.00000000 0.00
CG2O1 CG311 NG2R53 5 107.000000 418.400000 0.00000000 0.00
CG2RC0 CG3C52 NG2R53 5 111.600000 878.640000 0.00000000 0.00
CG2RC0 NG2R51 CG321 5 125.900000 585.760000 0.00000000 0.00
CG311 NG2R53 CG3C52 5 116.000000 317.984000 0.00000000 0.00
CG2O1 NG2S1 CG2O1 5 124.600000 391.622400 0.00000000 0.00

[ dihedraltypes ]
; i j k l func phi0 kphi mult
NG2S1 CG2O1 CG311 NG2R53 9 0.000000 2.510400 1
OG2D1 CG2O1 CG311 NG2R53 9 0.000000 0.000000 1
CG311 CG2O1 NG2S1 CG2O1 9 180.000000 3.096160 2
CG321 CG2O1 NG2S1 CG2O1 9 180.000000 6.903600 2
OG2D1 CG2O1 NG2S1 CG2O1 9 180.000000 2.426720 2
NG2R53 CG2R53 CG2RC0 CG2R61 9 180.000000 6.276000 2
NG2R53 CG2R53 CG2RC0 CG2RC0 9 180.000000 37.656000 2
OG2D1 CG2R53 CG2RC0 CG2R61 9 180.000000 5.020800 2
OG2D1 CG2R53 CG2RC0 CG2RC0 9 180.000000 5.020800 2
CG2RC0 CG2R53 NG2R53 CG311 9 0.000000 6.694400 1
CG2RC0 CG2R53 NG2R53 CG311 9 180.000000 10.460000 2
CG2RC0 CG2R53 NG2R53 CG3C52 9 0.000000 6.694400 1
CG2RC0 CG2R53 NG2R53 CG3C52 9 180.000000 10.460000 2
CG2O1 CG2R61 CG2R61 CG2RC0 9 180.000000 12.970400 2
CG2R61 CG2R61 CG2RC0 CG2R53 9 180.000000 6.276000 2
HGR61 CG2R61 CG2RC0 CG2R53 9 180.000000 0.000000 2
CG2R53 CG2RC0 CG2RC0 CG2R61 9 180.000000 6.276000 2
CG2R53 CG2RC0 CG2RC0 CG3C52 9 180.000000 20.920000 2
CG2R61 CG2RC0 CG3C52 NG2R53 9 0.000000 3.765600 3
CG2RC0 CG2RC0 CG3C52 NG2R53 9 180.000000 4.184000 3
CG2R61 CG2RC0 NG2R51 CG321 9 180.000000 0.047698 2
CG2R67 CG2RC0 NG2R51 CG321 9 180.000000 46.024000 2
NG2R53 CG311 CG321 CG321 9 0.000000 0.836800 3
CG2O1 CG311 NG2R53 CG2R53 9 180.000000 0.000000 1
CG2O1 CG311 NG2R53 CG3C52 9 0.000000 6.473066 1
CG2O1 CG311 NG2R53 CG3C52 9 180.000000 4.879381 2
CG321 CG311 NG2R53 CG3C52 9 0.000000 12.808061 1
CG321 CG311 NG2R53 CG3C52 9 180.000000 0.467771 2
HGA1 CG311 NG2R53 CG3C52 9 0.000000 1.757280 3
CG2O1 CG321 NG2R51 CG2RC0 9 180.000000 3.743425 1
CG2O1 CG321 NG2R51 CG2RC0 9 180.000000 1.776526 2
CG2O1 CG321 NG2R51 CG2RC0 9 0.000000 2.025893 3
HGA2 CG321 NG2R51 CG2RC0 9 0.000000 0.000000 3
CG2RC0 CG3C52 NG2R53 CG2R53 9 180.000000 9.665040 3
CG2RC0 CG3C52 NG2R53 CG311 9 180.000000 9.665040 3
HGA2 CG3C52 NG2R53 CG311 9 0.000000 0.000000 3

[ dihedraltypes ]
; ‘improper’ dihedrals
; i j k l func phi0 kphi
CG2R53 CG2RC0 NG2R53 OG2D1 2 0.000000 753.120000

If you can help to fix this, I would appreciate it very much.

Thank you!

Mahesh

2

All [ <bond,angle,dihedral,...>types ] sections must come before the first [ molecule types ] section, see Common errors when using GROMACS - GROMACS 2024.3 documentation.

The other errors you are getting before is because of the same error, i.e., the parameters of bonded interactions are not defined when you use them. Move bonded and non-bonded [ ...types ] sections to a separate file and include that after the forcefield.itp in your topology file.

3

Thank you. But I am still getting this error: ERROR 1 [file unl.itp, line 7]:
Atoms in the .top are not numbered consecutively from 1 (rather, atomnr =
1, while at->nr = 1371)

Can you please help?

Mahesh

4

Have you looked at the atom numbering in the itp file?