# Ligand submission problem/covalent docking **URL:** \ **Category:** HADDOCK\ **Created:** [June 23, 2023, 8:12am UTC](https://ask.bioexcel.eu/t/ligand-submission-problem-covalent-docking/4393 "2023-06-23T08:12:42Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![sdraga](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@sdraga](https://ask.bioexcel.eu/u/sdraga)\ **Post date:** [June 23, 2023, 8:12am UTC](https://ask.bioexcel.eu/t/ligand-submission-problem-covalent-docking/4393/1 "2023-06-23T08:12:42Z")
Hello everyone, I’m attempting to dock a covalent molecule, using HADDOCK 2.4 (done this before with different ligands). However, in this case, it appears that the ligand file cannot be submitted for some reason. I’ve submitted the original PDB file, generated by Obabel, to both `pdb_uniquename` and `pdb_tidy`, followed by `pdb_validate` and everything _seems_ ok, but I get the following error: ```auto Error in PDB file. Could not parse the PDB file at line 0: record unknown (COMPN) ``` I’ve also looked at my previous ligand submissions in terms of file structure, and they also contain these lines and worked with no issues. Also tried to remove the first line(s) and just leave the HETATM records, but then get: ```auto Error in PDB file. Could not parse the PDB file at line 0: record unknown (HETAT) ``` Below is a part of the file, so that one can get an impression of the overall structure: ```auto COMPND UNNAMED AUTHOR GENERATED BY OPEN BABEL 2.3.2 HETATM 1 C1 LIG 1 -1.706 8.945 -5.791 1.00 0.00 C HETATM 2 N1 LIG 1 -0.591 8.318 -5.071 1.00 0.00 N HETATM 3 C2 LIG 1 -0.900 8.258 -3.639 1.00 0.00 C HETATM 4 C3 LIG 1 0.235 7.727 -2.813 1.00 0.00 C HETATM 5 C4 LIG 1 0.142 6.581 -2.123 1.00 0.00 C HETATM 6 C5 LIG 1 1.218 6.133 -1.206 1.00 0.00 C HETATM 7 N2 LIG 1 1.157 4.829 -0.803 1.00 0.00 N HETATM 8 C6 LIG 1 0.596 3.715 -1.449 1.00 0.00 C HETATM 9 C7 LIG 1 -0.020 2.707 -0.704 1.00 0.00 C HETATM 10 O1 LIG 1 -0.336 2.739 0.629 1.00 0.00 O HETATM 11 C8 LIG 1 -0.726 3.990 1.187 1.00 0.00 C HETATM 12 C9 LIG 1 -0.325 1.492 -1.324 1.00 0.00 C HETATM 13 C10 LIG 1 0.014 1.223 -2.640 1.00 0.00 C HETATM 14 N3 LIG 1 -0.211 -0.009 -3.098 1.00 0.00 N HETATM 15 C11 LIG 1 0.182 -0.267 -4.346 1.00 0.00 C HETATM 16 N4 LIG 1 0.741 0.611 -5.179 1.00 0.00 N HETATM 17 C12 LIG 1 0.927 1.868 -4.728 1.00 0.00 C HETATM 18 N5 LIG 1 1.484 2.821 -5.632 1.00 0.00 N HETATM 19 C13 LIG 1 1.556 2.594 -7.031 1.00 0.00 C HETATM 20 C14 LIG 1 0.442 2.101 -7.735 1.00 0.00 C HETATM 21 C15 LIG 1 0.536 1.664 -9.071 1.00 0.00 C HETATM 22 S1 LIG 1 -0.843 0.696 -9.666 1.00 0.00 S HETATM 23 O2 LIG 1 -1.417 0.086 -8.490 1.00 0.00 O HETATM 24 N6 LIG 1 -2.061 1.773 -10.335 1.00 0.00 N HETATM 25 C16 LIG 1 -1.547 2.841 -11.298 1.00 0.00 C HETATM 26 C17 LIG 1 -0.961 2.271 -12.586 1.00 0.00 C ``` Any help would be appreciated, Many thanks, S ---
**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:** [June 23, 2023, 10:08am UTC](https://ask.bioexcel.eu/t/ligand-submission-problem-covalent-docking/4393/2 "2023-06-23T10:08:10Z")
Try loading it into e.g. pymol and saving it again as a PDF formatted file. May-be something weird with the format or the file encoding… Did you defined it correctly as ligand when submitting it? ---
**Author:** ![sdraga](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@sdraga](https://ask.bioexcel.eu/u/sdraga)\ **Post date:** [June 23, 2023, 10:24am UTC](https://ask.bioexcel.eu/t/ligand-submission-problem-covalent-docking/4393/3 "2023-06-23T10:24:39Z")
Dear Professor Bonvin, On spot advice as always - it work by saving again via Pymol. Yes, it was originally submited as Ligand. Thank you!