# Haddock2.4 error **URL:** \ **Category:** Uncategorized\ **Created:** [March 16, 2023, 5:37pm UTC](https://ask.bioexcel.eu/t/haddock2-4-error/4184 "2023-03-16T17:37:49Z")\ **Posts on this page:** 11\ **Page:** 1
**Author:** ![aap](https://avatars.discourse-cdn.com/v4/letter/a/82dd89/32.png) [@aap](https://ask.bioexcel.eu/u/aap)\ **Post date:** [March 16, 2023, 5:37pm UTC](https://ask.bioexcel.eu/t/haddock2-4-error/4184/1 "2023-03-16T17:37:49Z")
I am getting following error with my PDB file. Surprisingly using the same file I could perform my docking experiments around 4 months back on Haddock2.4 Error in PDB file. Issue when parsing the PDB file at line **730**. Your PDB contains an known residue **PDBLine: HETATM 187 N MSE A 385 95.929 69.782 8.214 1.00 48.94 N** that should be using ATOM record, please check the [HADDOCK library](https://wenmr.science.uu.nl/haddock2.4/library) for a list of supported modified residues. ---
**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:** [March 16, 2023, 6:05pm UTC](https://ask.bioexcel.eu/t/haddock2-4-error/4184/2 "2023-03-16T18:05:50Z")
Convert MSE from HETATM to ATOM ---
**Author:** ![aap](https://avatars.discourse-cdn.com/v4/letter/a/82dd89/32.png) [@aap](https://ask.bioexcel.eu/u/aap)\ **Post date:** [March 16, 2023, 6:13pm UTC](https://ask.bioexcel.eu/t/haddock2-4-error/4184/3 "2023-03-16T18:13:28Z")
Did that but this time the error is Error in PDB file. Issue when parsing the PDB file at line **730**. ATOM/HETATM line does not meet the expected format ---
**Author:** ![aap](https://avatars.discourse-cdn.com/v4/letter/a/82dd89/32.png) [@aap](https://ask.bioexcel.eu/u/aap)\ **Post date:** [March 16, 2023, 6:14pm UTC](https://ask.bioexcel.eu/t/haddock2-4-error/4184/4 "2023-03-16T18:14:30Z")
Moreover I have used the same structure earlier in Haddock2.4 and there was no problem. I am facing this problem from last month or so ---
**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:** [March 16, 2023, 6:43pm UTC](https://ask.bioexcel.eu/t/haddock2-4-error/4184/5 "2023-03-16T18:43:25Z")
Be careful of keeping the correct formatting! HETATM is six characters while ATOM is only four, I.e. two spaces are needed to keep the column formatting ---
**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:** [March 17, 2023, 10:26am UTC](https://ask.bioexcel.eu/t/haddock2-4-error/4184/6 "2023-03-17T10:26:30Z")
The server and the validation performed is always evolving. As explained already when modifying a PDB file make sure to mess up the column formatting. ---
**Author:** ![aap](https://avatars.discourse-cdn.com/v4/letter/a/82dd89/32.png) [@aap](https://ask.bioexcel.eu/u/aap)\ **Post date:** [March 17, 2023, 2:29pm UTC](https://ask.bioexcel.eu/t/haddock2-4-error/4184/7 "2023-03-17T14:29:58Z")
Thank you for your feedback, but I did the formatting very carefully as explained…still problem persists. Facing the same problem for few other structures also ---
**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:** [March 17, 2023, 2:57pm UTC](https://ask.bioexcel.eu/t/haddock2-4-error/4184/8 "2023-03-17T14:57:05Z")
Share then one of those problematic PDB file ---
**Author:** ![aap](https://avatars.discourse-cdn.com/v4/letter/a/82dd89/32.png) [@aap](https://ask.bioexcel.eu/u/aap)\ **Post date:** [March 17, 2023, 3:55pm UTC](https://ask.bioexcel.eu/t/haddock2-4-error/4184/9 "2023-03-17T15:55:12Z")
The structure I am using is a PDB structure 4JJY and chain A of this structure ([RCSB PDB - 4JJY: Alix V domain](https://www.rcsb.org/structure/4JJY)) Unfortunately as I am a new user, I am not able to attach a file. Please suggest a way out for this issue. 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:** [March 18, 2023, 8:58am UTC](https://ask.bioexcel.eu/t/haddock2-4-error/4184/10 "2023-03-18T08:58:08Z")
No problem on my side once I edited the HETATM/ATOM issue (and cleaned the PDB to only keep chainA) See attached PDB file [4JJY-A.pdb](https://ask.bioexcel.eu/uploads/short-url/pNJzFcsw0xJnF0oKppl1s9Aint.pdb) (213.6 KB) ---
**Author:** ![aap](https://avatars.discourse-cdn.com/v4/letter/a/82dd89/32.png) [@aap](https://ask.bioexcel.eu/u/aap)\ **Post date:** [March 18, 2023, 3:30pm UTC](https://ask.bioexcel.eu/t/haddock2-4-error/4184/11 "2023-03-18T15:30:51Z")
Thanks a lot…its working now.