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.
The chloride atom is most likely the problem - not supported by PRODRG - is this the first ligand you tried containing a chloride?
Couple of months ago, I had run a ligand containing chlorine and faced no problem
Nothing changed to the PRODRG part generating the topologies and parameters for ligands.
Would you recommend anything else that I could possibly try?
can you share the PDB file of your ligand?
Did you also try deleting the hydrogens from the input PDB file?
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