Hello Professor,
Thank you so much for your reply! I edited manually according to the following link: PDB format - Plouf This was presented in another reply (Ligand Formatting - #2 by VGPReys) . I edited my ligands accordingly, and now the docking jobs were queued on HADDOCK server successfully. I went back and tried to use PDB-Tools Web once more to check whether I can use validate tool for ligands I generated. I uploaded my pdb and used only pdb_validate, checked Tidy mark, and clicked Run. I got the following error: " Last tool output is not PDB format and tidy cannot be applied" . Then, I used the tool without marking Tidy and got the result. Thank you so much for your time and help!