David Cabezas González Can you share the PDBQT and PDB files? There are a couple of reasons why this may happen, e.g.:

1. The CONECT records are missing from the final PDB file. They are either discarded when generating the PDBQT, or when converting back to PDB. The easiest fix would be to simply copy the original CONECT records from the original PDB to the final PDB.

2. The ligand was renamed (probably during PDBQT generation) and the ligand ID in the CONECT records does not anymore match the ligand ID in the ATOM records. Simplest fix would be to rename the ligand back to its original name in the final PDB.

I had simillar problems with a ligand. We think that the pdb file misslink the bonds when converted from pdbqt because of its atoms proximity after structural optimization. We simply used other program to get a different optimizaed conformation of the ligand and procide the docking with it. I recomend using MOPAC.

This happens sometimes with the ligands during conversion to pdbqt......

Try to generate pdb format from Chimera and convert the same to pdbqt through openbabel then use for docking as a ligand...... This will solve the purpose..... I had the same issue once.....

This happen due to the issues in the CONNECT part in the pdb file.