I'm confused on ligand optimization . I have used gabedit software for this, Very first I have drew my compound after that I choose these option in gabedit

• Set atom types,Molecular Mechanics(look for lower energy conformation)
• MM gradient point optimization
• Minimization-Molecular dynamics conformational search-MD,gradients,MM option for force fields

After that I have saved my final optimized compound PDB format for chimera Auto-dock vina Docking

But when I see these compounds some compounds bonds breaking , only showing atoms. Not a proper structure as earlier inserted one . why is it? So please help me , Do I need to select any option here or Do I need to do mopac optimization for docking in chimera Autodockvina?

Further, I did optimization in chemsketch software also. I used Hex software for docking Sir. But I got better results from gabedit optimized structure (Followed above steps) rather than chemsetch optimization.

Now I'm confusing my optimization part. Those I followed steps are correct or not .. Please help me