Hello, I’m new to docking and I’m trying to create a topology file for Cyanidin 3-glucoside as a ligand using CGenFF. I’ve added hydrogens and sorted my mol2 file, but I’m getting a warning “no valid resonance structure found” and the generated str file is empty. Has anyone else encountered this issue? Any suggestions on how to fix this problem would be greatly appreciated!
here is content of mol2 file:
@MOLECULE
cyanidin
54 56 0 0 0
SMALL
GASTEIGER
@ATOM
1 CL 8.5991 1.7143 0.0000 Cl 1 cyanidin 0.0000
2 O 5.1350 -1.2857 0.0000 O.3 1 cyanidin -0.3313
3 O 6.8671 -1.2857 0.0000 O.3 1 cyanidin -0.4571
4 O 5.1350 -4.2857 0.0000 O.3 1 cyanidin -0.3864
5 O 3.4030 -3.2857 0.0000 O.3 1 cyanidin -0.3865
6 O 6.8671 -3.2857 0.0000 O.3 1 cyanidin -0.3829
7 O 2.5369 -1.7857 0.0000 O.3 1 cyanidin -0.3924
8 O 7.7331 1.2143 0.0000 O.2 1 cyanidin -0.4509
9 O 4.2308 1.2112 0.0000 O.3 1 cyanidin -0.5059
10 O 5.9889 4.2836 0.0000 O.3 1 cyanidin -0.5065
11 O 9.4651 -2.7857 0.0000 O.3 1 cyanidin -0.5033
12 O 11.1972 -1.7857 0.0000 O.3 1 cyanidin -0.5033
13 C 5.1350 -3.2857 0.0000 C.3 1 cyanidin 0.1152
14 C 4.2690 -2.7857 0.0000 C.3 1 cyanidin 0.1120
15 C 6.0010 -2.7857 0.0000 C.3 1 cyanidin 0.1454
16 C 4.2690 -1.7857 0.0000 C.3 1 cyanidin 0.1140
17 C 6.0010 -1.7857 0.0000 C.3 1 cyanidin 0.2310
18 C 3.4030 -1.2857 0.0000 C.3 1 cyanidin 0.0731
19 C 6.8671 -0.2857 0.0000 C.ar 1 cyanidin 0.1674
20 C 7.7331 0.2143 0.0000 C.ar 1 cyanidin 0.1772
21 C 6.0010 0.2143 0.0000 C.ar 1 cyanidin -0.0020
22 C 6.0010 1.2143 0.0000 C.ar 1 cyanidin 0.0624
23 C 6.8671 1.7143 0.0000 C.ar 1 cyanidin 0.1428
24 C 8.5991 -0.2857 0.0000 C.ar 1 cyanidin 0.0246
25 C 5.0910 1.7212 0.0000 C.ar 1 cyanidin 0.1311
26 C 6.8831 2.7558 0.0000 C.ar 1 cyanidin 0.0230
27 C 8.5991 -1.2857 0.0000 C.ar 1 cyanidin -0.0058
28 C 9.4651 0.2143 0.0000 C.ar 1 cyanidin -0.0473
29 C 5.0830 2.7628 0.0000 C.ar 1 cyanidin 0.0221
30 C 5.9851 3.2836 0.0000 C.ar 1 cyanidin 0.1239
31 C 9.4651 -1.7857 0.0000 C.ar 1 cyanidin 0.1589
32 C 10.3312 -0.2857 0.0000 C.ar 1 cyanidin -0.0159
33 C 10.3312 -1.2857 0.0000 C.ar 1 cyanidin 0.1583
34 H 4.5981 -3.5957 0.0000 H 1 cyanidin 0.0648
35 H 4.2690 -3.4057 0.0000 H 1 cyanidin 0.0647
36 H 6.0010 -3.4057 0.0000 H 1 cyanidin 0.0683
37 H 4.2690 -1.1657 0.0000 H 1 cyanidin 0.0647
38 H 6.0010 -1.1657 0.0000 H 1 cyanidin 0.1084
39 H 3.8015 -0.8107 0.0000 H 1 cyanidin 0.0584
40 H 3.0044 -0.8107 0.0000 H 1 cyanidin 0.0584
41 H 4.5981 -4.5957 0.0000 H 1 cyanidin 0.2100
42 H 3.4030 -3.9057 0.0000 H 1 cyanidin 0.2100
43 H 6.8671 -3.9057 0.0000 H 1 cyanidin 0.2102
44 H 2.0000 -1.4757 0.0000 H 1 cyanidin 0.2095
45 H 5.4641 -0.0957 0.0000 H 1 cyanidin 0.0663
46 H 7.4236 3.0596 0.0000 H 1 cyanidin 0.0691
47 H 8.0622 -1.5957 0.0000 H 1 cyanidin 0.0662
48 H 9.4651 0.8343 0.0000 H 1 cyanidin 0.0626
49 H 4.5449 3.0707 0.0000 H 1 cyanidin 0.0691
50 H 10.8681 0.0243 0.0000 H 1 cyanidin 0.0655
51 H 3.6904 1.5150 0.0000 H 1 cyanidin 0.2922
52 H 5.4532 4.5957 0.0000 H 1 cyanidin 0.2921
53 H 10.0021 -3.0957 0.0000 H 1 cyanidin 0.2923
54 H 11.7341 -1.4757 0.0000 H 1 cyanidin 0.2923
@UNITY_ATOM_ATTR
1 1
charge -1
@BOND
1 2 16 1
2 2 17 1
3 3 17 1
4 3 19 1
5 4 13 1
6 4 41 1
7 5 14 1
8 5 42 1
9 6 15 1
10 6 43 1
11 7 18 1
12 7 44 1
13 8 20 ar
14 8 23 ar
15 9 25 1
16 9 51 1
17 10 30 1
18 10 52 1
19 11 31 1
20 11 53 1
21 12 33 1
22 12 54 1
23 13 14 1
24 13 15 1
25 13 34 1
26 14 16 1
27 14 35 1
28 15 17 1
29 15 36 1
30 16 18 1
31 16 37 1
32 17 38 1
33 18 39 1
34 18 40 1
35 19 20 ar
36 19 21 ar
37 20 24 1
38 21 22 ar
39 21 45 1
40 22 23 ar
41 22 25 ar
42 23 26 ar
43 24 27 ar
44 24 28 ar
45 25 29 ar
46 26 30 ar
47 26 46 1
48 27 31 ar
49 27 47 1
50 28 32 ar
51 28 48 1
52 29 30 ar
53 29 49 1
54 31 33 ar
55 32 33 ar
56 32 50 1