# Failed advanced refinemet **URL:** \ **Category:** HADDOCK\ **Created:** [July 28, 2021, 1:27pm UTC](https://ask.bioexcel.eu/t/failed-advanced-refinemet/3184 "2021-07-28T13:27:09Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![aysebercinb](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/aysebercinb/32/268_2.png) [@aysebercinb](https://ask.bioexcel.eu/u/aysebercinb)\ **Post date:** [July 28, 2021, 1:27pm UTC](https://ask.bioexcel.eu/t/failed-advanced-refinemet/3184/1 "2021-07-28T13:27:09Z")
Hi, I am performing Advanced refinement on HADDOCK2.2 Multi-body interface server. I have 6 different states of the same system. My input pdb file formats are all the same but my 3 of runs failed in topology generation. I attached my pdb files here and tagged the failed pdb as “failed”. I am writing the error message below: **Status: FAILED** There was an error in the topology generation. The most likely cause is an unusual format of your PDB structures. I thought the error was due to clash in the structure, but also I though HADDOCK refinement will remove this clash. How can I solve this case? Thanks [cluster1-successful.pdb](https://ask.bioexcel.eu/uploads/short-url/7dN1fYTjzfB5CEynQ9hGLoWm0d3.pdb) (398.5 KB) [cluster2-failed.pdb](https://ask.bioexcel.eu/uploads/short-url/iFuZhywXIJAfTYeeh6kWaPoF1rh.pdb) (398.5 KB) ---
**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:** [July 28, 2021, 2:04pm UTC](https://ask.bioexcel.eu/t/failed-advanced-refinemet/3184/2 "2021-07-28T14:04:22Z")
May-be try first the HADDOCK2.4 refinement interface - it has several options for refinement. Some of those are described in the following preprint: - T Neijenhuis, S.C. van Keulen and A.M.J.J. Bonvin. [Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4](https://doi.org/10.1101/2021.06.22.449462). _bioRxiv_ doi:2021.06.22.449462 (2021). ---
**Author:** ![aysebercinb](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/aysebercinb/32/268_2.png) [@aysebercinb](https://ask.bioexcel.eu/u/aysebercinb)\ **Post date:** [July 28, 2021, 2:25pm UTC](https://ask.bioexcel.eu/t/failed-advanced-refinemet/3184/3 "2021-07-28T14:25:53Z")
Sure, but the reason of I am using HADDOCK2.2 is the output file includes the energy-per-residue (ene-residue.disp) file. In my previous runs, I could not find this file HADDOCK2.4 output. Thank you ---
**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:** [July 28, 2021, 2:52pm UTC](https://ask.bioexcel.eu/t/failed-advanced-refinemet/3184/4 "2021-07-28T14:52:53Z")
We have now added that option to the 2.4 refinement interface (needs expert/guru access). Looking at your structure, the SAM ligand could the be problem… And note that HADDOCK2.4 uses a different (PDB-like) nomenclature for nucleic acids. ---
**Author:** ![aysebercinb](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/aysebercinb/32/268_2.png) [@aysebercinb](https://ask.bioexcel.eu/u/aysebercinb)\ **Post date:** [July 28, 2021, 3:21pm UTC](https://ask.bioexcel.eu/t/failed-advanced-refinemet/3184/5 "2021-07-28T15:21:36Z")
It is very nice to hear that! But now in 2.4 refinement interface, I got this error: The following error occurred when processing one of your PDB file: Instances of ligand DA do not contain the same atoms. And now, I guess I solved the error on 2.2 server. I removed the hydrogens on structure and I submitted it. My status is “Running” now. 🤓 Thank you for your all answers 🙂 ---
**Author:** ![aysebercinb](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/aysebercinb/32/268_2.png) [@aysebercinb](https://ask.bioexcel.eu/u/aysebercinb)\ **Post date:** [July 28, 2021, 3:58pm UTC](https://ask.bioexcel.eu/t/failed-advanced-refinemet/3184/7 "2021-07-28T15:58:09Z")
I think the 2.4 error is due to the P, OP1 and OP2 atoms. And the 2.2 run give error again 😕 ---
**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:** [July 28, 2021, 7:15pm UTC](https://ask.bioexcel.eu/t/failed-advanced-refinemet/3184/8 "2021-07-28T19:15:36Z")
Tweaked your PDB file. Deleted the SAM hydrogen atoms. [cluster2-failed.pdb](https://ask.bioexcel.eu/uploads/short-url/jdrDykEYjeCL5rLqE4idrZjktb3.pdb) (396.2 KB) Seems working (so far): [https://bianca.science.uu.nl/haddock2.4/run/1111111111/76329-test](https://bianca.science.uu.nl/haddock2.4/run/1111111111/76329-test) ---
**Author:** ![aysebercinb](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/aysebercinb/32/268_2.png) [@aysebercinb](https://ask.bioexcel.eu/u/aysebercinb)\ **Post date:** [July 30, 2021, 1:20pm UTC](https://ask.bioexcel.eu/t/failed-advanced-refinemet/3184/9 "2021-07-30T13:20:00Z")
Thank you @amjjbonvin I am submitting my other runs by this way.