Grompp Fatal error: Invalid bond type

swamybioinfo · October 15, 2020, 5:08am

GROMACS version:version 2020.3
GROMACS modification: Yes/No

Dear Sir,
I am unable find the solution for following error

gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

Fatal error:
Invalid bond type 0

The following file is lig1.itp file.

; Created by cgenff_charmm2gmx.py

[ moleculetype ]
; Name nrexcl
LIG1 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 LIG1 rtp LIG1 q qsum
1 CG3C51 1 LIG1 C1 1 0.084 12.011 ;
2 NG3C51 1 LIG1 N1 2 -0.479 14.007 ;
3 OG311 1 LIG1 O1 3 -0.652 15.999 ;
4 CG311 1 LIG1 C2 4 -0.055 12.011 ;
5 NG311 1 LIG1 N2 5 -0.727 14.007 ;
6 OG311 1 LIG1 O2 6 -0.649 15.999 ;
7 CG3C52 1 LIG1 C3 7 0.093 12.011 ;
8 OG311 1 LIG1 O3 8 -0.617 15.999 ;
9 CG3C52 1 LIG1 C4 9 -0.212 12.011 ;
10 OG311 1 LIG1 O4 10 -0.617 15.999 ;
11 CG3C52 1 LIG1 C5 11 -0.214 12.011 ;
12 CG321 1 LIG1 C6 12 -0.168 12.011 ;
13 CG321 1 LIG1 C7 13 -0.168 12.011 ;
14 CG321 1 LIG1 C8 14 0.122 12.011 ;
15 CG321 1 LIG1 C9 15 -0.178 12.011 ;
16 CG321 1 LIG1 C10 16 -0.178 12.011 ;
17 CG311 1 LIG1 C11 17 0.006 12.011 ;
18 CG311 1 LIG1 C12 18 0.137 12.011 ;
19 CG321 1 LIG1 C13 19 -0.163 12.011 ;
20 CG311 1 LIG1 C14 20 -0.096 12.011 ;
21 CG321 1 LIG1 C15 21 -0.169 12.011 ;
22 CG311 1 LIG1 C16 22 0.138 12.011 ;
23 CG321 1 LIG1 C17 23 -0.179 12.011 ;
24 CG311 1 LIG1 C18 24 0.408 12.011 ;
25 HGA1 1 LIG1 H01 25 0.090 1.008 ;
26 HGA1 1 LIG1 H02 26 0.090 1.008 ;
27 HGPAM1 1 LIG1 H03 27 0.347 1.008 ;
28 HGA2 1 LIG1 H04 28 0.090 1.008 ;
29 HGP1 1 LIG1 H05 29 0.369 1.008 ;
30 HGA2 1 LIG1 H06 30 0.090 1.008 ;
31 HGP1 1 LIG1 H07 31 0.369 1.008 ;
32 HGA2 1 LIG1 H08 32 0.090 1.008 ;
33 HGA2 1 LIG1 H09 33 0.090 1.008 ;
34 HGA2 1 LIG1 H14 34 0.090 1.008 ;
35 HGA2 1 LIG1 H15 35 0.090 1.008 ;
36 HGA2 1 LIG1 H16 36 0.090 1.008 ;
37 HGA2 1 LIG1 H17 37 0.090 1.008 ;
38 HGA1 1 LIG1 H18 38 0.090 1.008 ;
39 HGA1 1 LIG1 H19 39 0.090 1.008 ;
40 HGA2 1 LIG1 H20 40 0.090 1.008 ;
41 HGA1 1 LIG1 H21 41 0.090 1.008 ;
42 HGA2 1 LIG1 H22 42 0.090 1.008 ;
43 HGA1 1 LIG1 H23 43 0.090 1.008 ;
44 HGA2 1 LIG1 H24 44 0.090 1.008 ;
45 HGA1 1 LIG1 H25 45 0.090 1.008 ;
46 HGA2 1 LIG1 H1 46 0.090 1.008 ;
47 HGA2 1 LIG1 H2 47 0.090 1.008 ;
48 HGA2 1 LIG1 H3 48 0.090 1.008 ;
49 HGA2 1 LIG1 H4 49 0.090 1.008 ;
50 HGA2 1 LIG1 H5 50 0.090 1.008 ;
51 HGA2 1 LIG1 H6 51 0.090 1.008 ;
52 HGA2 1 LIG1 H7 52 0.090 1.008 ;
53 HGA2 1 LIG1 H8 53 0.090 1.008 ;
54 HGA2 1 LIG1 H9 54 0.090 1.008 ;
55 HGA2 1 LIG1 H10 55 0.090 1.008 ;
56 HGA2 1 LIG1 H11 56 0.090 1.008 ;
57 HGP1 1 LIG1 H12 57 0.419 1.008 ;
58 HGP1 1 LIG1 H13 58 0.419 1.008 ;

[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1 ; CG3C51 NG3C51
1 9 1 ; CG3C51 CG3C52
1 14 1 ; CG3C51 CG321
1 25 1 ; CG3C51 HGA1
2 4 1 ; NG3C51 CG311
2 7 1 ; NG3C51 CG3C52
3 57 1 ; OG311 HGP1
3 18 1 ; OG311 CG311
4 12 1 ; CG311 CG321
4 13 1 ; CG311 CG321
4 26 1 ; CG311 HGA1
5 14 1 ; NG311 CG321
5 27 1 ; NG311 HGPAM1
5 17 1 ; NG311 CG311
6 58 1 ; OG311 HGP1
6 22 1 ; OG311 CG311
7 11 1 ; CG3C52 CG3C52
7 28 1 ; CG3C52 HGA2
7 46 1 ; CG3C52 HGA2
8 24 1 ; OG311 CG311
8 29 1 ; OG311 HGP1
9 11 1 ; CG3C52 CG3C52
9 30 1 ; CG3C52 HGA2
9 47 1 ; CG3C52 HGA2
10 24 1 ; OG311 CG311
10 31 1 ; OG311 HGP1
11 32 1 ; CG3C52 HGA2
11 48 1 ; CG3C52 HGA2
12 15 1 ; CG321 CG321
12 33 1 ; CG321 HGA2
12 49 1 ; CG321 HGA2
13 16 1 ; CG321 CG321
13 34 1 ; CG321 HGA2
13 50 1 ; CG321 HGA2
14 35 1 ; CG321 HGA2
14 51 1 ; CG321 HGA2
15 18 1 ; CG321 CG311
15 36 1 ; CG321 HGA2
15 52 1 ; CG321 HGA2
16 18 1 ; CG321 CG311
16 37 1 ; CG321 HGA2
16 53 1 ; CG321 HGA2
17 19 1 ; CG311 CG321
17 21 1 ; CG311 CG321
17 38 1 ; CG311 HGA1
18 39 1 ; CG311 HGA1
19 20 1 ; CG321 CG311
19 40 1 ; CG321 HGA2
19 54 1 ; CG321 HGA2
20 22 1 ; CG311 CG311
20 24 1 ; CG311 CG311
20 41 1 ; CG311 HGA1
21 23 1 ; CG321 CG321
21 42 1 ; CG321 HGA2
21 55 1 ; CG321 HGA2
22 23 1 ; CG311 CG321
22 43 1 ; CG311 HGA1
23 44 1 ; CG321 HGA2
23 56 1 ; CG321 HGA2
24 45 1 ; CG311 HGA1

[ pairs ]
; ai aj funct c0 c1 c2 c3
1 12 1
1 13 1
1 26 1
1 28 1
1 46 1
1 27 1
1 17 1
1 32 1
1 48 1
2 30 1
2 47 1
2 5 1
2 35 1
2 51 1
2 15 1
2 33 1
2 49 1
2 16 1
2 34 1
2 50 1
2 32 1
2 48 1
3 12 1
3 36 1
3 52 1
3 13 1
3 37 1
3 53 1
4 9 1
4 14 1
4 25 1
4 11 1
4 28 1
4 46 1
4 18 1
4 36 1
4 52 1
4 37 1
4 53 1
5 9 1
5 25 1
5 20 1
5 40 1
5 54 1
5 23 1
5 42 1
5 55 1
6 19 1
6 24 1
6 41 1
6 21 1
6 44 1
6 56 1
7 14 1
7 25 1
7 12 1
7 13 1
7 26 1
7 30 1
7 47 1
8 31 1
8 19 1
8 22 1
8 41 1
9 35 1
9 51 1
9 28 1
9 46 1
10 29 1
10 19 1
10 22 1
10 41 1
11 14 1
11 25 1
12 16 1
12 34 1
12 50 1
12 39 1
13 15 1
13 33 1
13 49 1
13 39 1
14 30 1
14 47 1
14 19 1
14 21 1
14 38 1
15 57 1
15 26 1
15 37 1
15 53 1
16 57 1
16 26 1
16 36 1
16 52 1
17 35 1
17 51 1
17 22 1
17 24 1
17 41 1
17 44 1
17 56 1
18 33 1
18 49 1
18 34 1
18 50 1
19 27 1
19 23 1
19 42 1
19 55 1
19 43 1
19 45 1
20 58 1
20 29 1
20 31 1
20 21 1
20 38 1
20 44 1
20 56 1
21 27 1
21 40 1
21 54 1
21 43 1
22 40 1
22 54 1
22 45 1
22 42 1
22 55 1
23 58 1
23 38 1
23 24 1
23 41 1
24 40 1
24 54 1
24 43 1
25 30 1
25 47 1
25 35 1
25 51 1
26 33 1
26 49 1
26 34 1
26 50 1
27 35 1
27 51 1
27 38 1
28 32 1
28 48 1
29 45 1
30 32 1
30 48 1

10 24 20 5 ; OG311 CG311 CG311
10 24 45 5 ; OG311 CG311 HGA1
20 24 45 5 ; CG311 CG311 HGA1

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
9 1 2 4 9 ; CG3C52 CG3C51 NG3C51 CG311
9 1 2 7 9 ; CG3C52 CG3C51 NG3C51 CG3C52
14 1 2 4 9 ; CG321 CG3C51 NG3C51 CG311
14 1 2 7 9 ; CG321 CG3C51 NG3C51 CG3C52
25 1 2 4 9 ; HGA1 CG3C51 NG3C51 CG311
25 1 2 7 9 ; HGA1 CG3C51 NG3C51 CG3C52
2 1 9 11 9 ; NG3C51 CG3C51 CG3C52 CG3C52
2 1 9 30 9 ; NG3C51 CG3C51 CG3C52 HGA2
2 1 9 47 9 ; NG3C51 CG3C51 CG3C52 HGA2
14 1 9 11 9 ; CG321 CG3C51 CG3C52 CG3C52
14 1 9 30 9 ; CG321 CG3C51 CG3C52 HGA2
14 1 9 47 9 ; CG321 CG3C51 CG3C52 HGA2
25 1 9 11 9 ; HGA1 CG3C51 CG3C52 CG3C52
25 1 9 30 9 ; HGA1 CG3C51 CG3C52 HGA2
25 1 9 47 9 ; HGA1 CG3C51 CG3C52 HGA2
2 1 14 5 9 ; NG3C51 CG3C51 CG321 NG311
2 1 14 35 9 ; NG3C51 CG3C51 CG321 HGA2
2 1 14 51 9 ; NG3C51 CG3C51 CG321 HGA2
9 1 14 5 9 ; CG3C52 CG3C51 CG321 NG311
9 1 14 35 9 ; CG3C52 CG3C51 CG321 HGA2
9 1 14 51 9 ; CG3C52 CG3C51 CG321 HGA2
25 1 14 5 9 ; HGA1 CG3C51 CG321 NG311
25 1 14 35 9 ; HGA1 CG3C51 CG321 HGA2
25 1 14 51 9 ; HGA1 CG3C51 CG321 HGA2
1 2 4 12 9 ; CG3C51 NG3C51 CG311 CG321
1 2 4 13 9 ; CG3C51 NG3C51 CG311 CG321
1 2 4 26 9 ; CG3C51 NG3C51 CG311 HGA1
7 2 4 12 9 ; CG3C52 NG3C51 CG311 CG321
7 2 4 13 9 ; CG3C52 NG3C51 CG311 CG321
7 2 4 26 9 ; CG3C52 NG3C51 CG311 HGA1
1 2 7 11 9 ; CG3C51 NG3C51 CG3C52 CG3C52
1 2 7 28 9 ; CG3C51 NG3C51 CG3C52 HGA2
1 2 7 46 9 ; CG3C51 NG3C51 CG3C52 HGA2
4 2 7 11 9 ; CG311 NG3C51 CG3C52 CG3C52
4 2 7 28 9 ; CG311 NG3C51 CG3C52 HGA2
4 2 7 46 9 ; CG311 NG3C51 CG3C52 HGA2
57 3 18 15 9 ; HGP1 OG311 CG311 CG321
57 3 18 16 9 ; HGP1 OG311 CG311 CG321
57 3 18 39 9 ; HGP1 OG311 CG311 HGA1
2 4 12 15 9 ; NG3C51 CG311 CG321 CG321
2 4 12 33 9 ; NG3C51 CG311 CG321 HGA2
2 4 12 49 9 ; NG3C51 CG311 CG321 HGA2
13 4 12 15 9 ; CG321 CG311 CG321 CG321
13 4 12 33 9 ; CG321 CG311 CG321 HGA2
13 4 12 49 9 ; CG321 CG311 CG321 HGA2
26 4 12 15 9 ; HGA1 CG311 CG321 CG321
26 4 12 33 9 ; HGA1 CG311 CG321 HGA2
26 4 12 49 9 ; HGA1 CG311 CG321 HGA2
2 4 13 16 9 ; NG3C51 CG311 CG321 CG321
2 4 13 34 9 ; NG3C51 CG311 CG321 HGA2
2 4 13 50 9 ; NG3C51 CG311 CG321 HGA2
12 4 13 16 9 ; CG321 CG311 CG321 CG321
12 4 13 34 9 ; CG321 CG311 CG321 HGA2
12 4 13 50 9 ; CG321 CG311 CG321 HGA2
26 4 13 16 9 ; HGA1 CG311 CG321 CG321
26 4 13 34 9 ; HGA1 CG311 CG321 HGA2
26 4 13 50 9 ; HGA1 CG311 CG321 HGA2
27 5 14 1 9 ; HGPAM1 NG311 CG321 CG3C51
27 5 14 35 9 ; HGPAM1 NG311 CG321 HGA2
27 5 14 51 9 ; HGPAM1 NG311 CG321 HGA2
17 5 14 1 9 ; CG311 NG311 CG321 CG3C51
17 5 14 35 9 ; CG311 NG311 CG321 HGA2
17 5 14 51 9 ; CG311 NG311 CG321 HGA2
14 5 17 19 9 ; CG321 NG311 CG311 CG321
14 5 17 21 9 ; CG321 NG311 CG311 CG321
14 5 17 38 9 ; CG321 NG311 CG311 HGA1
27 5 17 19 9 ; HGPAM1 NG311 CG311 CG321
27 5 17 21 9 ; HGPAM1 NG311 CG311 CG321
27 5 17 38 9 ; HGPAM1 NG311 CG311 HGA1
58 6 22 20 9 ; HGP1 OG311 CG311 CG311
58 6 22 23 9 ; HGP1 OG311 CG311 CG321
58 6 22 43 9 ; HGP1 OG311 CG311 HGA1
2 7 11 9 9 ; NG3C51 CG3C52 CG3C52 CG3C52
2 7 11 32 9 ; NG3C51 CG3C52 CG3C52 HGA2
2 7 11 48 9 ; NG3C51 CG3C52 CG3C52 HGA2
28 7 11 9 9 ; HGA2 CG3C52 CG3C52 CG3C52
28 7 11 32 9 ; HGA2 CG3C52 CG3C52 HGA2
28 7 11 48 9 ; HGA2 CG3C52 CG3C52 HGA2
46 7 11 9 9 ; HGA2 CG3C52 CG3C52 CG3C52
46 7 11 32 9 ; HGA2 CG3C52 CG3C52 HGA2
46 7 11 48 9 ; HGA2 CG3C52 CG3C52 HGA2
29 8 24 10 9 ; HGP1 OG311 CG311 OG311
29 8 24 20 9 ; HGP1 OG311 CG311 CG311
29 8 24 45 9 ; HGP1 OG311 CG311 HGA1
1 9 11 7 9 ; CG3C51 CG3C52 CG3C52 CG3C52
1 9 11 32 9 ; CG3C51 CG3C52 CG3C52 HGA2
1 9 11 48 9 ; CG3C51 CG3C52 CG3C52 HGA2
30 9 11 7 9 ; HGA2 CG3C52 CG3C52 CG3C52
30 9 11 32 9 ; HGA2 CG3C52 CG3C52 HGA2
30 9 11 48 9 ; HGA2 CG3C52 CG3C52 HGA2
47 9 11 7 9 ; HGA2 CG3C52 CG3C52 CG3C52
47 9 11 32 9 ; HGA2 CG3C52 CG3C52 HGA2
47 9 11 48 9 ; HGA2 CG3C52 CG3C52 HGA2
31 10 24 8 9 ; HGP1 OG311 CG311 OG311
31 10 24 20 9 ; HGP1 OG311 CG311 CG311
31 10 24 45 9 ; HGP1 OG311 CG311 HGA1
4 12 15 18 9 ; CG311 CG321 CG321 CG311
4 12 15 36 9 ; CG311 CG321 CG321 HGA2
4 12 15 52 9 ; CG311 CG321 CG321 HGA2
33 12 15 18 9 ; HGA2 CG321 CG321 CG311
33 12 15 36 9 ; HGA2 CG321 CG321 HGA2
33 12 15 52 9 ; HGA2 CG321 CG321 HGA2
49 12 15 18 9 ; HGA2 CG321 CG321 CG311
49 12 15 36 9 ; HGA2 CG321 CG321 HGA2
49 12 15 52 9 ; HGA2 CG321 CG321 HGA2
4 13 16 18 9 ; CG311 CG321 CG321 CG311
4 13 16 37 9 ; CG311 CG321 CG321 HGA2
4 13 16 53 9 ; CG311 CG321 CG321 HGA2
34 13 16 18 9 ; HGA2 CG321 CG321 CG311
34 13 16 37 9 ; HGA2 CG321 CG321 HGA2
34 13 16 53 9 ; HGA2 CG321 CG321 HGA2
50 13 16 18 9 ; HGA2 CG321 CG321 CG311
50 13 16 37 9 ; HGA2 CG321 CG321 HGA2
50 13 16 53 9 ; HGA2 CG321 CG321 HGA2
12 15 18 3 9 ; CG321 CG321 CG311 OG311
12 15 18 16 9 ; CG321 CG321 CG311 CG321
12 15 18 39 9 ; CG321 CG321 CG311 HGA1
36 15 18 3 9 ; HGA2 CG321 CG311 OG311
36 15 18 16 9 ; HGA2 CG321 CG311 CG321
36 15 18 39 9 ; HGA2 CG321 CG311 HGA1
52 15 18 3 9 ; HGA2 CG321 CG311 OG311
52 15 18 16 9 ; HGA2 CG321 CG311 CG321
52 15 18 39 9 ; HGA2 CG321 CG311 HGA1
13 16 18 3 9 ; CG321 CG321 CG311 OG311
13 16 18 15 9 ; CG321 CG321 CG311 CG321
13 16 18 39 9 ; CG321 CG321 CG311 HGA1
37 16 18 3 9 ; HGA2 CG321 CG311 OG311
37 16 18 15 9 ; HGA2 CG321 CG311 CG321
37 16 18 39 9 ; HGA2 CG321 CG311 HGA1
53 16 18 3 9 ; HGA2 CG321 CG311 OG311
53 16 18 15 9 ; HGA2 CG321 CG311 CG321
53 16 18 39 9 ; HGA2 CG321 CG311 HGA1
5 17 19 20 9 ; NG311 CG311 CG321 CG311
5 17 19 40 9 ; NG311 CG311 CG321 HGA2
5 17 19 54 9 ; NG311 CG311 CG321 HGA2
21 17 19 20 9 ; CG321 CG311 CG321 CG311
21 17 19 40 9 ; CG321 CG311 CG321 HGA2
21 17 19 54 9 ; CG321 CG311 CG321 HGA2
38 17 19 20 9 ; HGA1 CG311 CG321 CG311
38 17 19 40 9 ; HGA1 CG311 CG321 HGA2
38 17 19 54 9 ; HGA1 CG311 CG321 HGA2
5 17 21 23 9 ; NG311 CG311 CG321 CG321
5 17 21 42 9 ; NG311 CG311 CG321 HGA2
5 17 21 55 9 ; NG311 CG311 CG321 HGA2
19 17 21 23 9 ; CG321 CG311 CG321 CG321
19 17 21 42 9 ; CG321 CG311 CG321 HGA2
19 17 21 55 9 ; CG321 CG311 CG321 HGA2
38 17 21 23 9 ; HGA1 CG311 CG321 CG321
38 17 21 42 9 ; HGA1 CG311 CG321 HGA2
38 17 21 55 9 ; HGA1 CG311 CG321 HGA2
17 19 20 22 9 ; CG311 CG321 CG311 CG311
17 19 20 24 9 ; CG311 CG321 CG311 CG311
17 19 20 41 9 ; CG311 CG321 CG311 HGA1
40 19 20 22 9 ; HGA2 CG321 CG311 CG311
40 19 20 24 9 ; HGA2 CG321 CG311 CG311
40 19 20 41 9 ; HGA2 CG321 CG311 HGA1
54 19 20 22 9 ; HGA2 CG321 CG311 CG311
54 19 20 24 9 ; HGA2 CG321 CG311 CG311
54 19 20 41 9 ; HGA2 CG321 CG311 HGA1
19 20 22 6 9 ; CG321 CG311 CG311 OG311
19 20 22 23 9 ; CG321 CG311 CG311 CG321
19 20 22 43 9 ; CG321 CG311 CG311 HGA1
24 20 22 6 9 ; CG311 CG311 CG311 OG311
24 20 22 23 9 ; CG311 CG311 CG311 CG321
24 20 22 43 9 ; CG311 CG311 CG311 HGA1
41 20 22 6 9 ; HGA1 CG311 CG311 OG311
41 20 22 23 9 ; HGA1 CG311 CG311 CG321
41 20 22 43 9 ; HGA1 CG311 CG311 HGA1
19 20 24 8 9 ; CG321 CG311 CG311 OG311
19 20 24 10 9 ; CG321 CG311 CG311 OG311
19 20 24 45 9 ; CG321 CG311 CG311 HGA1
22 20 24 8 9 ; CG311 CG311 CG311 OG311
22 20 24 10 9 ; CG311 CG311 CG311 OG311
22 20 24 45 9 ; CG311 CG311 CG311 HGA1
41 20 24 8 9 ; HGA1 CG311 CG311 OG311
41 20 24 10 9 ; HGA1 CG311 CG311 OG311
41 20 24 45 9 ; HGA1 CG311 CG311 HGA1
17 21 23 22 9 ; CG311 CG321 CG321 CG311
17 21 23 44 9 ; CG311 CG321 CG321 HGA2
17 21 23 56 9 ; CG311 CG321 CG321 HGA2
42 21 23 22 9 ; HGA2 CG321 CG321 CG311
42 21 23 44 9 ; HGA2 CG321 CG321 HGA2
42 21 23 56 9 ; HGA2 CG321 CG321 HGA2
55 21 23 22 9 ; HGA2 CG321 CG321 CG311
55 21 23 44 9 ; HGA2 CG321 CG321 HGA2
55 21 23 56 9 ; HGA2 CG321 CG321 HGA2
6 22 23 21 9 ; OG311 CG311 CG321 CG321
6 22 23 44 9 ; OG311 CG311 CG321 HGA2
6 22 23 56 9 ; OG311 CG311 CG321 HGA2
20 22 23 21 9 ; CG311 CG311 CG321 CG321
20 22 23 44 9 ; CG311 CG311 CG321 HGA2
20 22 23 56 9 ; CG311 CG311 CG321 HGA2
43 22 23 21 9 ; HGA1 CG311 CG321 CG321
43 22 23 44 9 ; HGA1 CG311 CG321 HGA2
43 22 23 56 9 ; HGA1 CG311 CG321 HGA2

lig1.gro
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
58
1LIG1 C1 1 21.421 18.273 25.981
1LIG1 N1 2 21.391 18.209 26.101
1LIG1 O1 3 21.293 17.669 26.167
1LIG1 C2 4 21.361 18.073 26.124
1LIG1 N2 5 21.371 18.099 25.821
1LIG1 O2 6 21.348 17.844 25.327
1LIG1 C3 7 21.402 18.302 26.203
1LIG1 O3 8 21.699 18.056 25.433
1LIG1 C4 9 21.451 18.405 26.013
1LIG1 O4 10 21.589 17.963 25.266
.
.
.
.

1LIG1   C17   23  21.253  17.909  25.530
1LIG1   C18   24  21.596  18.003  25.385
1LIG1   H01   25  21.411  18.234  25.880
1LIG1   H02   26  21.276  18.057  26.191
1LIG1   H03   27  21.418  18.030  25.879
1LIG1   H04   28  21.398  18.339  26.305
1LIG1   H05   29  21.730  18.004  25.507
1LIG1   H06   30  21.479  18.480  25.939
1LIG1   H07   31  21.530  17.888  25.261
1LIG1   H08   32  21.447  18.518  26.204
1LIG1   H09   33  21.194  18.071  26.166
1LIG1   H14   34  21.426  18.051  26.275
1LIG1   H15   35  21.406  18.104  25.832
1LIG1   H16   36  21.161  17.849  26.184
1LIG1   H17   37  21.400  17.826  26.302
1LIG1   H18   38  21.392  18.152  25.676
1LIG1   H19   39  21.266  17.900  26.171
1LIG1   H20   40  21.402  17.992  25.553
1LIG1   H21   41  21.497  17.969  25.371
1LIG1   H22   42  21.350  18.020  25.620
1LIG1   H23   43  21.430  17.992  25.406
1LIG1   H24   44  21.250  18.003  25.474
1LIG1   H25   45  21.652  17.989  25.292
1LIG1    H1   46  21.383  18.272  26.305
1LIG1    H2   47  21.480  18.482  25.942
1LIG1    H3   48  21.454  18.516  26.205
1LIG1    H4   49  21.165  18.082  26.032
1LIG1    H5   50  21.550  18.035  26.221
1LIG1    H6   51  21.476  18.272  25.774
1LIG1    H7   52  21.123  17.840  26.061
1LIG1    H8   53  21.507  17.794  26.249
1LIG1    H9   54  21.568  18.105  25.633
1LIG1   H10   55  21.174  17.964  25.720
1LIG1   H11   56  21.165  17.852  25.503
1LIG1   H12   57  21.207  17.639  26.131
1LIG1   H13   58  21.269  17.788  25.324

0.00000 0.00000 0.00000

alevilla · October 15, 2020, 7:26am

Hi,
The error indicates that you have a mistake in the topology.
From a quick look to your lig.itp I have noticed that angle are under the section [ pairs ] that is wrong. Add the header [ angles ] before the definition of the angles.
Here you can find more on the topology syntax http://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html?highlight=topology%20table
Best regards
Alessandra

swamybioinfo · October 15, 2020, 7:30am

Dear Sir,

please check the lig1.itp
; Created by cgenff_charmm2gmx.py

[ moleculetype ]
; Name nrexcl
LIG1 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 LIG1 rtp LIG1 q qsum
1 CG3C51 1 LIG1 C1 1 0.084 12.011 ;
2 NG3C51 1 LIG1 N1 2 -0.479 14.007 ;
3 OG311 1 LIG1 O1 3 -0.652 15.999 ;
4 CG311 1 LIG1 C2 4 -0.055 12.011 ;
5 NG311 1 LIG1 N2 5 -0.727 14.007 ;
6 OG311 1 LIG1 O2 6 -0.649 15.999 ;
7 CG3C52 1 LIG1 C3 7 0.093 12.011 ;
8 OG311 1 LIG1 O3 8 -0.617 15.999 ;
9 CG3C52 1 LIG1 C4 9 -0.212 12.011 ;
10 OG311 1 LIG1 O4 10 -0.617 15.999 ;
11 CG3C52 1 LIG1 C5 11 -0.214 12.011 ;
12 CG321 1 LIG1 C6 12 -0.168 12.011 ;
13 CG321 1 LIG1 C7 13 -0.168 12.011 ;
14 CG321 1 LIG1 C8 14 0.122 12.011 ;
15 CG321 1 LIG1 C9 15 -0.178 12.011 ;
16 CG321 1 LIG1 C10 16 -0.178 12.011 ;
17 CG311 1 LIG1 C11 17 0.006 12.011 ;
18 CG311 1 LIG1 C12 18 0.137 12.011 ;
19 CG321 1 LIG1 C13 19 -0.163 12.011 ;
20 CG311 1 LIG1 C14 20 -0.096 12.011 ;
21 CG321 1 LIG1 C15 21 -0.169 12.011 ;
22 CG311 1 LIG1 C16 22 0.138 12.011 ;
23 CG321 1 LIG1 C17 23 -0.179 12.011 ;
24 CG311 1 LIG1 C18 24 0.408 12.011 ;
25 HGA1 1 LIG1 H01 25 0.090 1.008 ;
26 HGA1 1 LIG1 H02 26 0.090 1.008 ;
27 HGPAM1 1 LIG1 H03 27 0.347 1.008 ;
28 HGA2 1 LIG1 H04 28 0.090 1.008 ;
29 HGP1 1 LIG1 H05 29 0.369 1.008 ;
30 HGA2 1 LIG1 H06 30 0.090 1.008 ;
31 HGP1 1 LIG1 H07 31 0.369 1.008 ;
32 HGA2 1 LIG1 H08 32 0.090 1.008 ;
33 HGA2 1 LIG1 H09 33 0.090 1.008 ;
34 HGA2 1 LIG1 H14 34 0.090 1.008 ;
35 HGA2 1 LIG1 H15 35 0.090 1.008 ;
36 HGA2 1 LIG1 H16 36 0.090 1.008 ;
37 HGA2 1 LIG1 H17 37 0.090 1.008 ;
38 HGA1 1 LIG1 H18 38 0.090 1.008 ;
39 HGA1 1 LIG1 H19 39 0.090 1.008 ;
40 HGA2 1 LIG1 H20 40 0.090 1.008 ;
41 HGA1 1 LIG1 H21 41 0.090 1.008 ;
42 HGA2 1 LIG1 H22 42 0.090 1.008 ;
43 HGA1 1 LIG1 H23 43 0.090 1.008 ;
44 HGA2 1 LIG1 H24 44 0.090 1.008 ;
45 HGA1 1 LIG1 H25 45 0.090 1.008 ;
46 HGA2 1 LIG1 H1 46 0.090 1.008 ;
47 HGA2 1 LIG1 H2 47 0.090 1.008 ;
48 HGA2 1 LIG1 H3 48 0.090 1.008 ;
49 HGA2 1 LIG1 H4 49 0.090 1.008 ;
50 HGA2 1 LIG1 H5 50 0.090 1.008 ;
51 HGA2 1 LIG1 H6 51 0.090 1.008 ;
52 HGA2 1 LIG1 H7 52 0.090 1.008 ;
53 HGA2 1 LIG1 H8 53 0.090 1.008 ;
54 HGA2 1 LIG1 H9 54 0.090 1.008 ;
55 HGA2 1 LIG1 H10 55 0.090 1.008 ;
56 HGA2 1 LIG1 H11 56 0.090 1.008 ;
57 HGP1 1 LIG1 H12 57 0.419 1.008 ;
58 HGP1 1 LIG1 H13 58 0.419 1.008 ;

[ bonds ]
; ai aj funct c0 c1 c3
1 2 1
1 9 1
1 14 1
1 25 1
2 4 1
2 7 1
3 57 1
3 18 1
4 12 1
4 13 1
4 26 1
5 14 1
5 27 1
5 17 1
6 58 1
6 22 1
7 11 1
7 28 1
7 46 1
8 24 1
8 29 1
9 11 1
9 30 1
9 47 1
10 24 1
10 31 1
11 32 1
11 48 1
12 15 1
12 33 1
12 49 1
13 16 1
13 34 1
13 50 1
14 35 1
14 51 1
15 18 1
15 36 1
15 52 1
16 18 1
16 37 1
16 53 1
17 19 1
17 21 1
17 38 1
18 39 1
19 20 1
19 40 1
19 54 1
20 22 1
20 24 1
20 41 1
21 23 1
21 42 1
21 55 1
22 23 1
22 43 1
23 44 1
23 56 1
24 45 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 12 1
1 13 1
1 26 1
1 28 1
1 46 1
1 27 1
1 17 1
1 32 1
1 48 1
2 30 1
2 47 1
2 5 1
2 35 1
2 51 1
2 15 1
2 33 1
2 49 1
2 16 1
2 34 1
2 50 1
2 32 1
2 48 1
3 12 1
3 36 1
3 52 1
3 13 1
3 37 1
3 53 1
4 9 1
4 14 1
4 25 1
4 11 1
4 28 1
4 46 1
4 18 1
4 36 1
4 52 1
4 37 1
4 53 1
5 9 1
5 25 1
5 20 1
5 40 1
5 54 1
5 23 1
5 42 1
5 55 1
6 19 1
6 24 1
6 41 1
6 21 1
6 44 1
6 56 1
7 14 1
7 25 1
7 12 1
7 13 1
7 26 1
7 30 1
7 47 1
8 31 1
8 19 1
8 22 1
8 41 1
9 35 1
9 51 1
9 28 1
9 46 1
10 29 1
10 19 1
10 22 1
10 41 1
11 14 1
11 25 1
12 16 1
12 34 1
12 50 1
12 39 1
13 15 1
13 33 1
13 49 1
13 39 1
14 30 1
14 47 1
14 19 1
14 21 1
14 38 1
15 57 1
15 26 1
15 37 1
15 53 1
16 57 1
16 26 1
16 36 1
16 52 1
17 35 1
17 51 1
17 22 1
17 24 1
17 41 1
17 44 1
17 56 1
18 33 1
18 49 1
18 34 1
18 50 1
19 27 1
19 23 1
19 42 1
19 55 1
19 43 1
19 45 1
20 58 1
20 29 1
20 31 1
20 21 1
20 38 1
20 44 1
20 56 1
21 27 1
21 40 1
21 54 1
21 43 1
22 40 1
22 54 1
22 45 1
22 42 1
22 55 1
23 58 1
23 38 1
23 24 1
23 41 1
24 40 1
24 54 1
24 43 1
25 30 1
25 47 1
25 35 1
25 51 1
26 33 1
26 49 1
26 34 1
26 50 1
27 35 1
27 51 1
27 38 1
28 32 1
28 48 1
29 45 1
30 32 1
30 48 1
31 45 1
32 46 1
32 47 1
33 36 1
33 52 1
34 37 1
34 53 1
36 49 1
36 39 1
37 50 1
37 39 1
38 40 1
38 54 1
38 42 1
38 55 1
39 57 1
39 52 1
39 53 1
40 41 1
41 54 1
41 43 1
41 45 1
42 44 1
42 56 1
43 58 1
43 44 1
43 56 1
44 55 1
46 48 1
47 48 1
49 52 1
50 53 1
55 56 1

[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 9 5 ; NG3C51 CG3C51 CG3C52
2 1 14 5 ; NG3C51 CG3C51 CG321
2 1 25 5 ; NG3C51 CG3C51 HGA1
9 1 14 5 ; CG3C52 CG3C51 CG321
9 1 25 5 ; CG3C52 CG3C51 HGA1
14 1 25 5 ; CG321 CG3C51 HGA1
1 2 4 5 ; CG3C51 NG3C51 CG311
1 2 7 5 ; CG3C51 NG3C51 CG3C52
4 2 7 5 ; CG311 NG3C51 CG3C52
57 3 18 5 ; HGP1 OG311 CG311
2 4 12 5 ; NG3C51 CG311 CG321
2 4 13 5 ; NG3C51 CG311 CG321
2 4 26 5 ; NG3C51 CG311 HGA1
12 4 13 5 ; CG321 CG311 CG321
12 4 26 5 ; CG321 CG311 HGA1
13 4 26 5 ; CG321 CG311 HGA1
14 5 27 5 ; CG321 NG311 HGPAM1
14 5 17 5 ; CG321 NG311 CG311
27 5 17 5 ; HGPAM1 NG311 CG311
58 6 22 5 ; HGP1 OG311 CG311
2 7 11 5 ; NG3C51 CG3C52 CG3C52
2 7 28 5 ; NG3C51 CG3C52 HGA2
2 7 46 5 ; NG3C51 CG3C52 HGA2
11 7 28 5 ; CG3C52 CG3C52 HGA2
11 7 46 5 ; CG3C52 CG3C52 HGA2
28 7 46 5 ; HGA2 CG3C52 HGA2
24 8 29 5 ; CG311 OG311 HGP1
1 9 11 5 ; CG3C51 CG3C52 CG3C52
1 9 30 5 ; CG3C51 CG3C52 HGA2
1 9 47 5 ; CG3C51 CG3C52 HGA2
11 9 30 5 ; CG3C52 CG3C52 HGA2
11 9 47 5 ; CG3C52 CG3C52 HGA2
30 9 47 5 ; HGA2 CG3C52 HGA2
24 10 31 5 ; CG311 OG311 HGP1
7 11 9 5 ; CG3C52 CG3C52 CG3C52
7 11 32 5 ; CG3C52 CG3C52 HGA2
7 11 48 5 ; CG3C52 CG3C52 HGA2
9 11 32 5 ; CG3C52 CG3C52 HGA2
9 11 48 5 ; CG3C52 CG3C52 HGA2
32 11 48 5 ; HGA2 CG3C52 HGA2
4 12 15 5 ; CG311 CG321 CG321
4 12 33 5 ; CG311 CG321 HGA2
4 12 49 5 ; CG311 CG321 HGA2
15 12 33 5 ; CG321 CG321 HGA2
15 12 49 5 ; CG321 CG321 HGA2
33 12 49 5 ; HGA2 CG321 HGA2
4 13 16 5 ; CG311 CG321 CG321
4 13 34 5 ; CG311 CG321 HGA2
4 13 50 5 ; CG311 CG321 HGA2
16 13 34 5 ; CG321 CG321 HGA2
16 13 50 5 ; CG321 CG321 HGA2
34 13 50 5 ; HGA2 CG321 HGA2
1 14 5 5 ; CG3C51 CG321 NG311
1 14 35 5 ; CG3C51 CG321 HGA2
1 14 51 5 ; CG3C51 CG321 HGA2
5 14 35 5 ; NG311 CG321 HGA2
5 14 51 5 ; NG311 CG321 HGA2
35 14 51 5 ; HGA2 CG321 HGA2
12 15 18 5 ; CG321 CG321 CG311
12 15 36 5 ; CG321 CG321 HGA2
12 15 52 5 ; CG321 CG321 HGA2
18 15 36 5 ; CG311 CG321 HGA2
18 15 52 5 ; CG311 CG321 HGA2
36 15 52 5 ; HGA2 CG321 HGA2
13 16 18 5 ; CG321 CG321 CG311
13 16 37 5 ; CG321 CG321 HGA2
13 16 53 5 ; CG321 CG321 HGA2
18 16 37 5 ; CG311 CG321 HGA2
18 16 53 5 ; CG311 CG321 HGA2
37 16 53 5 ; HGA2 CG321 HGA2
5 17 19 5 ; NG311 CG311 CG321
5 17 21 5 ; NG311 CG311 CG321
5 17 38 5 ; NG311 CG311 HGA1
19 17 21 5 ; CG321 CG311 CG321
19 17 38 5 ; CG321 CG311 HGA1
21 17 38 5 ; CG321 CG311 HGA1
3 18 15 5 ; OG311 CG311 CG321
3 18 16 5 ; OG311 CG311 CG321
3 18 39 5 ; OG311 CG311 HGA1
15 18 16 5 ; CG321 CG311 CG321
15 18 39 5 ; CG321 CG311 HGA1
16 18 39 5 ; CG321 CG311 HGA1
17 19 20 5 ; CG311 CG321 CG311
17 19 40 5 ; CG311 CG321 HGA2
17 19 54 5 ; CG311 CG321 HGA2
20 19 40 5 ; CG311 CG321 HGA2
20 19 54 5 ; CG311 CG321 HGA2
40 19 54 5 ; HGA2 CG321 HGA2
19 20 22 5 ; CG321 CG311 CG311
19 20 24 5 ; CG321 CG311 CG311
19 20 41 5 ; CG321 CG311 HGA1
22 20 24 5 ; CG311 CG311 CG311
22 20 41 5 ; CG311 CG311 HGA1
24 20 41 5 ; CG311 CG311 HGA1
17 21 23 5 ; CG311 CG321 CG321
17 21 42 5 ; CG311 CG321 HGA2
17 21 55 5 ; CG311 CG321 HGA2
23 21 42 5 ; CG321 CG321 HGA2
23 21 55 5 ; CG321 CG321 HGA2
42 21 55 5 ; HGA2 CG321 HGA2
6 22 20 5 ; OG311 CG311 CG311
6 22 23 5 ; OG311 CG311 CG321
6 22 43 5 ; OG311 CG311 HGA1
20 22 23 5 ; CG311 CG311 CG321
20 22 43 5 ; CG311 CG311 HGA1
23 22 43 5 ; CG321 CG311 HGA1
21 23 22 5 ; CG321 CG321 CG311
21 23 44 5 ; CG321 CG321 HGA2
21 23 56 5 ; CG321 CG321 HGA2
22 23 44 5 ; CG311 CG321 HGA2
22 23 56 5 ; CG311 CG321 HGA2
44 23 56 5 ; HGA2 CG321 HGA2
8 24 10 5 ; OG311 CG311 OG311
8 24 20 5 ; OG311 CG311 CG311
8 24 45 5 ; OG311 CG311 HGA1
10 24 20 5 ; OG311 CG311 CG311
10 24 45 5 ; OG311 CG311 HGA1
20 24 45 5 ; CG311 CG311 HGA1

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
9 1 2 4 9 ; CG3C52 CG3C51 NG3C51 CG311
9 1 2 7 9 ; CG3C52 CG3C51 NG3C51 CG3C52
14 1 2 4 9 ; CG321 CG3C51 NG3C51 CG311
14 1 2 7 9 ; CG321 CG3C51 NG3C51 CG3C52
25 1 2 4 9 ; HGA1 CG3C51 NG3C51 CG311
25 1 2 7 9 ; HGA1 CG3C51 NG3C51 CG3C52
2 1 9 11 9 ; NG3C51 CG3C51 CG3C52 CG3C52
2 1 9 30 9 ; NG3C51 CG3C51 CG3C52 HGA2
2 1 9 47 9 ; NG3C51 CG3C51 CG3C52 HGA2
14 1 9 11 9 ; CG321 CG3C51 CG3C52 CG3C52
14 1 9 30 9 ; CG321 CG3C51 CG3C52 HGA2
14 1 9 47 9 ; CG321 CG3C51 CG3C52 HGA2
25 1 9 11 9 ; HGA1 CG3C51 CG3C52 CG3C52
25 1 9 30 9 ; HGA1 CG3C51 CG3C52 HGA2
25 1 9 47 9 ; HGA1 CG3C51 CG3C52 HGA2
2 1 14 5 9 ; NG3C51 CG3C51 CG321 NG311
2 1 14 35 9 ; NG3C51 CG3C51 CG321 HGA2
2 1 14 51 9 ; NG3C51 CG3C51 CG321 HGA2
9 1 14 5 9 ; CG3C52 CG3C51 CG321 NG311
9 1 14 35 9 ; CG3C52 CG3C51 CG321 HGA2
9 1 14 51 9 ; CG3C52 CG3C51 CG321 HGA2
25 1 14 5 9 ; HGA1 CG3C51 CG321 NG311
25 1 14 35 9 ; HGA1 CG3C51 CG321 HGA2
25 1 14 51 9 ; HGA1 CG3C51 CG321 HGA2
1 2 4 12 9 ; CG3C51 NG3C51 CG311 CG321
1 2 4 13 9 ; CG3C51 NG3C51 CG311 CG321
1 2 4 26 9 ; CG3C51 NG3C51 CG311 HGA1
7 2 4 12 9 ; CG3C52 NG3C51 CG311 CG321
7 2 4 13 9 ; CG3C52 NG3C51 CG311 CG321
7 2 4 26 9 ; CG3C52 NG3C51 CG311 HGA1
1 2 7 11 9 ; CG3C51 NG3C51 CG3C52 CG3C52
1 2 7 28 9 ; CG3C51 NG3C51 CG3C52 HGA2
1 2 7 46 9 ; CG3C51 NG3C51 CG3C52 HGA2
4 2 7 11 9 ; CG311 NG3C51 CG3C52 CG3C52
4 2 7 28 9 ; CG311 NG3C51 CG3C52 HGA2
4 2 7 46 9 ; CG311 NG3C51 CG3C52 HGA2
57 3 18 15 9 ; HGP1 OG311 CG311 CG321
57 3 18 16 9 ; HGP1 OG311 CG311 CG321
57 3 18 39 9 ; HGP1 OG311 CG311 HGA1
2 4 12 15 9 ; NG3C51 CG311 CG321 CG321
2 4 12 33 9 ; NG3C51 CG311 CG321 HGA2
2 4 12 49 9 ; NG3C51 CG311 CG321 HGA2
13 4 12 15 9 ; CG321 CG311 CG321 CG321
13 4 12 33 9 ; CG321 CG311 CG321 HGA2
13 4 12 49 9 ; CG321 CG311 CG321 HGA2
26 4 12 15 9 ; HGA1 CG311 CG321 CG321
26 4 12 33 9 ; HGA1 CG311 CG321 HGA2
26 4 12 49 9 ; HGA1 CG311 CG321 HGA2
2 4 13 16 9 ; NG3C51 CG311 CG321 CG321
2 4 13 34 9 ; NG3C51 CG311 CG321 HGA2
2 4 13 50 9 ; NG3C51 CG311 CG321 HGA2
12 4 13 16 9 ; CG321 CG311 CG321 CG321
12 4 13 34 9 ; CG321 CG311 CG321 HGA2
12 4 13 50 9 ; CG321 CG311 CG321 HGA2
26 4 13 16 9 ; HGA1 CG311 CG321 CG321
26 4 13 34 9 ; HGA1 CG311 CG321 HGA2
26 4 13 50 9 ; HGA1 CG311 CG321 HGA2
27 5 14 1 9 ; HGPAM1 NG311 CG321 CG3C51
27 5 14 35 9 ; HGPAM1 NG311 CG321 HGA2
27 5 14 51 9 ; HGPAM1 NG311 CG321 HGA2
17 5 14 1 9 ; CG311 NG311 CG321 CG3C51
17 5 14 35 9 ; CG311 NG311 CG321 HGA2
17 5 14 51 9 ; CG311 NG311 CG321 HGA2
14 5 17 19 9 ; CG321 NG311 CG311 CG321
14 5 17 21 9 ; CG321 NG311 CG311 CG321
14 5 17 38 9 ; CG321 NG311 CG311 HGA1
27 5 17 19 9 ; HGPAM1 NG311 CG311 CG321
27 5 17 21 9 ; HGPAM1 NG311 CG311 CG321
27 5 17 38 9 ; HGPAM1 NG311 CG311 HGA1
58 6 22 20 9 ; HGP1 OG311 CG311 CG311
58 6 22 23 9 ; HGP1 OG311 CG311 CG321
58 6 22 43 9 ; HGP1 OG311 CG311 HGA1
2 7 11 9 9 ; NG3C51 CG3C52 CG3C52 CG3C52
2 7 11 32 9 ; NG3C51 CG3C52 CG3C52 HGA2
2 7 11 48 9 ; NG3C51 CG3C52 CG3C52 HGA2
28 7 11 9 9 ; HGA2 CG3C52 CG3C52 CG3C52
28 7 11 32 9 ; HGA2 CG3C52 CG3C52 HGA2
28 7 11 48 9 ; HGA2 CG3C52 CG3C52 HGA2
46 7 11 9 9 ; HGA2 CG3C52 CG3C52 CG3C52
46 7 11 32 9 ; HGA2 CG3C52 CG3C52 HGA2
46 7 11 48 9 ; HGA2 CG3C52 CG3C52 HGA2
29 8 24 10 9 ; HGP1 OG311 CG311 OG311
29 8 24 20 9 ; HGP1 OG311 CG311 CG311
29 8 24 45 9 ; HGP1 OG311 CG311 HGA1
1 9 11 7 9 ; CG3C51 CG3C52 CG3C52 CG3C52
1 9 11 32 9 ; CG3C51 CG3C52 CG3C52 HGA2
1 9 11 48 9 ; CG3C51 CG3C52 CG3C52 HGA2
30 9 11 7 9 ; HGA2 CG3C52 CG3C52 CG3C52
30 9 11 32 9 ; HGA2 CG3C52 CG3C52 HGA2
30 9 11 48 9 ; HGA2 CG3C52 CG3C52 HGA2
47 9 11 7 9 ; HGA2 CG3C52 CG3C52 CG3C52
47 9 11 32 9 ; HGA2 CG3C52 CG3C52 HGA2
47 9 11 48 9 ; HGA2 CG3C52 CG3C52 HGA2
31 10 24 8 9 ; HGP1 OG311 CG311 OG311
31 10 24 20 9 ; HGP1 OG311 CG311 CG311
31 10 24 45 9 ; HGP1 OG311 CG311 HGA1
4 12 15 18 9 ; CG311 CG321 CG321 CG311
4 12 15 36 9 ; CG311 CG321 CG321 HGA2
4 12 15 52 9 ; CG311 CG321 CG321 HGA2
33 12 15 18 9 ; HGA2 CG321 CG321 CG311
33 12 15 36 9 ; HGA2 CG321 CG321 HGA2
33 12 15 52 9 ; HGA2 CG321 CG321 HGA2
49 12 15 18 9 ; HGA2 CG321 CG321 CG311
49 12 15 36 9 ; HGA2 CG321 CG321 HGA2
49 12 15 52 9 ; HGA2 CG321 CG321 HGA2
4 13 16 18 9 ; CG311 CG321 CG321 CG311
4 13 16 37 9 ; CG311 CG321 CG321 HGA2
4 13 16 53 9 ; CG311 CG321 CG321 HGA2
34 13 16 18 9 ; HGA2 CG321 CG321 CG311
34 13 16 37 9 ; HGA2 CG321 CG321 HGA2
34 13 16 53 9 ; HGA2 CG321 CG321 HGA2
50 13 16 18 9 ; HGA2 CG321 CG321 CG311
50 13 16 37 9 ; HGA2 CG321 CG321 HGA2
50 13 16 53 9 ; HGA2 CG321 CG321 HGA2
12 15 18 3 9 ; CG321 CG321 CG311 OG311
12 15 18 16 9 ; CG321 CG321 CG311 CG321
12 15 18 39 9 ; CG321 CG321 CG311 HGA1
36 15 18 3 9 ; HGA2 CG321 CG311 OG311
36 15 18 16 9 ; HGA2 CG321 CG311 CG321
36 15 18 39 9 ; HGA2 CG321 CG311 HGA1
52 15 18 3 9 ; HGA2 CG321 CG311 OG311
52 15 18 16 9 ; HGA2 CG321 CG311 CG321
52 15 18 39 9 ; HGA2 CG321 CG311 HGA1
13 16 18 3 9 ; CG321 CG321 CG311 OG311
13 16 18 15 9 ; CG321 CG321 CG311 CG321
13 16 18 39 9 ; CG321 CG321 CG311 HGA1
37 16 18 3 9 ; HGA2 CG321 CG311 OG311
37 16 18 15 9 ; HGA2 CG321 CG311 CG321
37 16 18 39 9 ; HGA2 CG321 CG311 HGA1
53 16 18 3 9 ; HGA2 CG321 CG311 OG311
53 16 18 15 9 ; HGA2 CG321 CG311 CG321
53 16 18 39 9 ; HGA2 CG321 CG311 HGA1
5 17 19 20 9 ; NG311 CG311 CG321 CG311
5 17 19 40 9 ; NG311 CG311 CG321 HGA2
5 17 19 54 9 ; NG311 CG311 CG321 HGA2
21 17 19 20 9 ; CG321 CG311 CG321 CG311
21 17 19 40 9 ; CG321 CG311 CG321 HGA2
21 17 19 54 9 ; CG321 CG311 CG321 HGA2
38 17 19 20 9 ; HGA1 CG311 CG321 CG311
38 17 19 40 9 ; HGA1 CG311 CG321 HGA2
38 17 19 54 9 ; HGA1 CG311 CG321 HGA2
5 17 21 23 9 ; NG311 CG311 CG321 CG321
5 17 21 42 9 ; NG311 CG311 CG321 HGA2
5 17 21 55 9 ; NG311 CG311 CG321 HGA2
19 17 21 23 9 ; CG321 CG311 CG321 CG321
19 17 21 42 9 ; CG321 CG311 CG321 HGA2
19 17 21 55 9 ; CG321 CG311 CG321 HGA2
38 17 21 23 9 ; HGA1 CG311 CG321 CG321
38 17 21 42 9 ; HGA1 CG311 CG321 HGA2
38 17 21 55 9 ; HGA1 CG311 CG321 HGA2
17 19 20 22 9 ; CG311 CG321 CG311 CG311
17 19 20 24 9 ; CG311 CG321 CG311 CG311
17 19 20 41 9 ; CG311 CG321 CG311 HGA1
40 19 20 22 9 ; HGA2 CG321 CG311 CG311
40 19 20 24 9 ; HGA2 CG321 CG311 CG311
40 19 20 41 9 ; HGA2 CG321 CG311 HGA1
54 19 20 22 9 ; HGA2 CG321 CG311 CG311
54 19 20 24 9 ; HGA2 CG321 CG311 CG311
54 19 20 41 9 ; HGA2 CG321 CG311 HGA1
19 20 22 6 9 ; CG321 CG311 CG311 OG311
19 20 22 23 9 ; CG321 CG311 CG311 CG321
19 20 22 43 9 ; CG321 CG311 CG311 HGA1
24 20 22 6 9 ; CG311 CG311 CG311 OG311
24 20 22 23 9 ; CG311 CG311 CG311 CG321
24 20 22 43 9 ; CG311 CG311 CG311 HGA1
41 20 22 6 9 ; HGA1 CG311 CG311 OG311
41 20 22 23 9 ; HGA1 CG311 CG311 CG321
41 20 22 43 9 ; HGA1 CG311 CG311 HGA1
19 20 24 8 9 ; CG321 CG311 CG311 OG311
19 20 24 10 9 ; CG321 CG311 CG311 OG311
19 20 24 45 9 ; CG321 CG311 CG311 HGA1
22 20 24 8 9 ; CG311 CG311 CG311 OG311
22 20 24 10 9 ; CG311 CG311 CG311 OG311
22 20 24 45 9 ; CG311 CG311 CG311 HGA1
41 20 24 8 9 ; HGA1 CG311 CG311 OG311
41 20 24 10 9 ; HGA1 CG311 CG311 OG311
41 20 24 45 9 ; HGA1 CG311 CG311 HGA1
17 21 23 22 9 ; CG311 CG321 CG321 CG311
17 21 23 44 9 ; CG311 CG321 CG321 HGA2
17 21 23 56 9 ; CG311 CG321 CG321 HGA2
42 21 23 22 9 ; HGA2 CG321 CG321 CG311
42 21 23 44 9 ; HGA2 CG321 CG321 HGA2
42 21 23 56 9 ; HGA2 CG321 CG321 HGA2
55 21 23 22 9 ; HGA2 CG321 CG321 CG311
55 21 23 44 9 ; HGA2 CG321 CG321 HGA2
55 21 23 56 9 ; HGA2 CG321 CG321 HGA2
6 22 23 21 9 ; OG311 CG311 CG321 CG321
6 22 23 44 9 ; OG311 CG311 CG321 HGA2
6 22 23 56 9 ; OG311 CG311 CG321 HGA2
20 22 23 21 9 ; CG311 CG311 CG321 CG321
20 22 23 44 9 ; CG311 CG311 CG321 HGA2
20 22 23 56 9 ; CG311 CG311 CG321 HGA2
43 22 23 21 9 ; HGA1 CG311 CG321 CG321
43 22 23 44 9 ; HGA1 CG311 CG321 HGA2
43 22 23 56 9 ; HGA1 CG311 CG321 HGA2

alevilla · October 15, 2020, 7:39am

Hi again,
what are exactly the errors when you run grompp without the option -maxwarn ?

I have also noticed that the last line of lig.gro is 0.000 0.000 0.000, did you put the molecule in the box ?

Best regards
Alessandra

swamybioinfo · October 15, 2020, 8:21am

Dear Sir,
I have created the lig.gro from the commands
python3 cgenff_charmm2gmx_py3_nx2.py LIG lig1_fix.mol2 lig.str charmm36-mar2019.ff
gmx editconf -f lig_ini.pdb -o lig.gro
gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0

gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

i am getting same error. as
Fatal error:
Invalid bond type 0

I am confused where is error.?

After generation of lig.gro i found all box vectors are 0 0 0. please check the images for lig.gro and protein.pro and coplex.gro for box vectors

box vectros as per protein.gro
1147SER OT116459 21.272 21.779 11.587
1147SER OT216460 21.297 21.808 11.627
8.23623 11.58355 16.02296

box vectors as per lig.gro
1LIG1 H12 57 21.207 17.639 26.131
1LIG1 H13 58 21.269 17.788 25.324
0.00000 0.00000 0.00000

Complex.gro box vectors
1LIG1 H12 57 21.207 17.639 26.131
1LIG1 H13 58 21.269 17.788 25.324
0.00000 0.00000 0.00000 8.23623 11.58355 16.02296 0.00000 0.00000 0.00000

later i followed the steps as per tutorial

Dr_DBW · October 16, 2020, 2:10am

What does your .top file contain?

swamybioinfo · October 16, 2020, 4:56pm

16459 OC 1147 SER OT1 16459 -0.67 15.9994
16460 OC 1147 SER OT2 16460 -0.67 15.9994 ; qtot -7

[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1
1 5 1
5 6 1
5 7 1
5 11 1
7 8 1
7 9 1
7 10 1
11 12 1
11 13 1
13 14 1
13 15 1
15 16 1
15 17 1
15 32 1
17 18 1
17 19 1
17 20 1
20 21 1
20 28 1
21 22 1
21 23 1
23 24 1
23 25 1
25 26 1

Dr_DBW · October 18, 2020, 9:48pm

That is not your .top file contents.

Topic		Replies	Views
How to solve 'Unknown bond_atomtype error'? User discussions	4	3814	May 26, 2020
Fatal error: There were 2 errors in input file(s) during ionization by using grompp module User discussions grompp	1	84	May 31, 2024
Grommp fatal error User discussions simulation-setup , gmx-grompp	1	167	December 6, 2023
Error in use of GROMPP User discussions	14	6000	August 8, 2022
Fatal error: There were 2 errors in input file(s) User discussions grompp , mdrun	13	2817	April 21, 2023

Grompp Fatal error: Invalid bond type

Related topics