# My pdb file of ligand has no errors-Ligand topology generation fails on the HADDOCK 2.4 web server **URL:** \ **Category:** HADDOCK\ **Created:** [October 13, 2026, 9:56am UTC](https://ask.bioexcel.eu/t/my-pdb-file-of-ligand-has-no-errors-ligand-topology-generation-fails-on-the-haddock-2-4-web-server/6289 "2026-10-13T09:56:37Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![Vibes](https://avatars.discourse-cdn.com/v4/letter/v/ecb155/32.png) [@Vibes](https://ask.bioexcel.eu/u/Vibes)\ **Post date:** [October 13, 2026, 9:56am UTC](https://ask.bioexcel.eu/t/my-pdb-file-of-ligand-has-no-errors-ligand-topology-generation-fails-on-the-haddock-2-4-web-server/6289/1 "2026-10-13T09:56:37Z")
My pdb file of ligand has no errors. Ligand topology generation fails on the HADDOCK 2.4 web server (run ID: 780651). My ligand is residue LIG, chain B, 33 atoms (incl. 3 Cl, 1 S), SMILES `O=S(=O)(OC[C@H]1O[C@H](CO)[C@@H](O)[C@@H]1O)OCC(Cl)(Cl)Cl`. The server loads a 23-atom LIG topology with starred atom names (C1\*…O2\*) and no Cl types, identical for a full 33-model ensemble and a single conformer, so my atoms are “not found in molecular structure” and CNS aborts with CODIMP-ERR missing impropers (CA3\* CA2\* CA4\* OA3\*). My earlier ligands, also named LIG, worked with no topology supplied. ---
**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:** [October 13, 2026, 10:21am UTC](https://ask.bioexcel.eu/t/my-pdb-file-of-ligand-has-no-errors-ligand-topology-generation-fails-on-the-haddock-2-4-web-server/6289/2 "2026-10-13T10:21:49Z")
The chloride atom is most likely the problem - not supported by PRODRG - is this the first ligand you tried containing a chloride? ---
**Author:** ![Vibes](https://avatars.discourse-cdn.com/v4/letter/v/ecb155/32.png) [@Vibes](https://ask.bioexcel.eu/u/Vibes)\ **Post date:** [October 13, 2026, 11:03am UTC](https://ask.bioexcel.eu/t/my-pdb-file-of-ligand-has-no-errors-ligand-topology-generation-fails-on-the-haddock-2-4-web-server/6289/3 "2026-10-13T11:03:14Z")
Couple of months ago, I had run a ligand containing chlorine and faced no problem ---
**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:** [October 13, 2026, 11:33am UTC](https://ask.bioexcel.eu/t/my-pdb-file-of-ligand-has-no-errors-ligand-topology-generation-fails-on-the-haddock-2-4-web-server/6289/4 "2026-10-13T11:33:34Z")
Nothing changed to the PRODRG part generating the topologies and parameters for ligands. ---
**Author:** ![Vibes](https://avatars.discourse-cdn.com/v4/letter/v/ecb155/32.png) [@Vibes](https://ask.bioexcel.eu/u/Vibes)\ **Post date:** [October 13, 2026, 11:47am UTC](https://ask.bioexcel.eu/t/my-pdb-file-of-ligand-has-no-errors-ligand-topology-generation-fails-on-the-haddock-2-4-web-server/6289/5 "2026-10-13T11:47:17Z")
Would you recommend anything else that I could possibly try? ---
**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:** [October 13, 2026, 11:59am UTC](https://ask.bioexcel.eu/t/my-pdb-file-of-ligand-has-no-errors-ligand-topology-generation-fails-on-the-haddock-2-4-web-server/6289/6 "2026-10-13T11:59:48Z")
can you share the PDB file of your ligand? Did you also try deleting the hydrogens from the input PDB file? ---
**Author:** ![Vibes](https://avatars.discourse-cdn.com/v4/letter/v/ecb155/32.png) [@Vibes](https://ask.bioexcel.eu/u/Vibes)\ **Post date:** [October 13, 2026, 12:23pm UTC](https://ask.bioexcel.eu/t/my-pdb-file-of-ligand-has-no-errors-ligand-topology-generation-fails-on-the-haddock-2-4-web-server/6289/7 "2026-10-13T12:23:43Z")
I tried docking run after removing the hydrogens and it still failed. I will send through the pdb file to your email id. Thank you very much for your help