# Bond length too high **URL:** \ **Category:** Uncategorized\ **Created:** [December 29, 2024, 2:18pm UTC](https://ask.bioexcel.eu/t/bond-length-too-high/5384 "2024-12-29T14:18:00Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![michael](https://avatars.discourse-cdn.com/v4/letter/m/4bbf92/32.png) [@michael](https://ask.bioexcel.eu/u/michael)\ **Post date:** [December 29, 2024, 2:18pm UTC](https://ask.bioexcel.eu/t/bond-length-too-high/5384/1 "2024-12-29T14:18:00Z")
Hi, Sometimes when I perform docking, the results seem illogical. For instance, the bond length exceeds 10 Å, which doesn’t make sense. What could be causing this? Thanks! ![Screenshot 2024-12-29 161523](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/2X/c/c700b0880961fd6ccceb3f0276aa5f05d414c4c9.png) ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [December 29, 2024, 2:51pm UTC](https://ask.bioexcel.eu/t/bond-length-too-high/5384/2 "2024-12-29T14:51:13Z")
Strange - does this only happen at a Pro-Pro connection? Can you share a link to the run if you used the server? ---
**Author:** ![michael](https://avatars.discourse-cdn.com/v4/letter/m/4bbf92/32.png) [@michael](https://ask.bioexcel.eu/u/michael)\ **Post date:** [December 29, 2024, 2:53pm UTC](https://ask.bioexcel.eu/t/bond-length-too-high/5384/3 "2024-12-29T14:53:09Z")
I didn’t use the surver I so far I only noticed this on Proline-proline ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [December 29, 2024, 6:34pm UTC](https://ask.bioexcel.eu/t/bond-length-too-high/5384/4 "2024-12-29T18:34:33Z")
Which haddock version are you using? And can you share your input PDB file for the peptide? ---
**Author:** ![michael](https://avatars.discourse-cdn.com/v4/letter/m/4bbf92/32.png) [@michael](https://ask.bioexcel.eu/u/michael)\ **Post date:** [December 29, 2024, 8:21pm UTC](https://ask.bioexcel.eu/t/bond-length-too-high/5384/5 "2024-12-29T20:21:36Z")
Thank you haddock2.4 I have 30 input files (for the peptide) but I can only upload 5. I noticed that also in some of the begin file the length is too large(even when it’s just Proline alone and not Pro-Pro) [frame\_840.pdb](https://ask.bioexcel.eu/uploads/short-url/4y1BguEozUFPvMNKNfrJN47EUU4.pdb) (11.4 KB) [frame\_993.pdb](https://ask.bioexcel.eu/uploads/short-url/5CVbZR2zgq85YwbUic0rB6wM8IU.pdb) (11.4 KB) [frame\_1004.pdb](https://ask.bioexcel.eu/uploads/short-url/ozLavNtAcdLPIvkfjRZsHBjyTqp.pdb) (11.4 KB) [frame\_724.pdb](https://ask.bioexcel.eu/uploads/short-url/v1Ep5Mu0a3geZLzXQJRd5Decl3I.pdb) (11.4 KB) [frame\_754.pdb](https://ask.bioexcel.eu/uploads/short-url/txC936UPOXQ7LeYt0frFPlz9ps9.pdb) (11.4 KB) ---
**Author:** ![michael](https://avatars.discourse-cdn.com/v4/letter/m/4bbf92/32.png) [@michael](https://ask.bioexcel.eu/u/michael)\ **Post date:** [December 31, 2024, 6:11pm UTC](https://ask.bioexcel.eu/t/bond-length-too-high/5384/6 "2024-12-31T18:11:29Z")
Hi, Do you have any ideas? Can I maybe email you all the files? Thank you very much ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [December 31, 2024, 7:47pm UTC](https://ask.bioexcel.eu/t/bond-length-too-high/5384/7 "2024-12-31T19:47:56Z")
There is something fishy with your PDB files. From the 5 you shared 993 gives a problem. After running it through our pdb-tools pdb\_tidy it runs fine. I suggest you process all you PDBs first with pdb\_tidy ---
**Author:** ![michael](https://avatars.discourse-cdn.com/v4/letter/m/4bbf92/32.png) [@michael](https://ask.bioexcel.eu/u/michael)\ **Post date:** [January 2, 2025, 4:52pm UTC](https://ask.bioexcel.eu/t/bond-length-too-high/5384/8 "2025-01-02T16:52:15Z")
Thank you very much I did your suggestion, but I am still getting the same error. Is it possible to send you the file run? ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [January 2, 2025, 7:23pm UTC](https://ask.bioexcel.eu/t/bond-length-too-high/5384/9 "2025-01-02T19:23:31Z")
Yes - send me a direct email with a link to download it (also the input data in that case). PS: I tested your system with haddock2.5