# Error in CGenFF: "No valid resonance structure found" **URL:** \ **Category:** User discussions\ **Tags:** topology\ **Created:** [September 26, 2024, 6:04am UTC](https://gromacs.bioexcel.eu/t/error-in-cgenff-no-valid-resonance-structure-found/10235 "2024-09-26T06:04:52Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![asoorni](https://avatars.discourse-cdn.com/v4/letter/a/90db22/32.png) [@asoorni](https://gromacs.bioexcel.eu/u/asoorni)\ **Post date:** [September 26, 2024, 6:04am UTC](https://gromacs.bioexcel.eu/t/error-in-cgenff-no-valid-resonance-structure-found/10235/1 "2024-09-26T06:04:52Z")
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 ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [September 26, 2024, 8:33am UTC](https://gromacs.bioexcel.eu/t/error-in-cgenff-no-valid-resonance-structure-found/10235/2 "2024-09-26T08:33:26Z")
Could you give some more context, please? From your description I don’t understand which tool is causing the problem. Are you using CHARMM GUI? ---
**Author:** ![asoorni](https://avatars.discourse-cdn.com/v4/letter/a/90db22/32.png) [@asoorni](https://gromacs.bioexcel.eu/u/asoorni)\ **Post date:** [September 26, 2024, 8:43am UTC](https://gromacs.bioexcel.eu/t/error-in-cgenff-no-valid-resonance-structure-found/10235/3 "2024-09-26T08:43:10Z")
Thank you for your reply. I am not using CHARMM GUI. I downloaded the coordinate file from PubChem and then added hydrogens using Avogadro. Next, I sorted the file using the Perl script and uploaded it to [https://cgenff.com/](https://cgenff.com/) to obtain the structure file. However, I encountered this issue during this process. ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [September 26, 2024, 8:59am UTC](https://gromacs.bioexcel.eu/t/error-in-cgenff-no-valid-resonance-structure-found/10235/4 "2024-09-26T08:59:49Z")
Then I think you should contact them.