Dear sir, energy minimization could help to resolve this problem.

So follow this order as,

01. Sketch out the ligands ( SD or .mol format)

02. Then open in Chem 3D, perform the energy minimization and save as pdb format. This makes the ligand more suitable for docking.

Then you can this ligand for docking.

Best regards.

To overcome this problem open output file into autodock and then save as pdb formate following the step

1.open autodock

2. Analyze--> open macromolecules slept proteinpdbqt file

3. ANnalyze--> open autodock vina result

4. Press ok

5. Select that ligand in left side and file --> save --> padb formate.

To solve this problem:

• Open the original SDF or PDB file of the ligand in Biovia Discovery Studio or PyMOL to ensure that the bond connectivity is intact.
• Use OpenBabel to reconvert the ligand back to PDB and check if any bonds are missing or broken.
• Ensure Biovia is set to "rebuild" or "infer" bond connectivity when loading files. This option can sometimes correct broken segments automatically.
• If the ligand breaks apart, you can manually edit the PDB file in a text editor to merge fragments. Ensure each segment has the same chain ID and residue number
• Use PyMOL or Chimera as alternative visualization tools if Biovia Discovery Studio does not handle the split poses well
• Also you can do energy minimization to avoid this problem