Hello! I made my ligand molecule using Chemdraw and Chem3D. Before docking, I made sure that the pdb file has the correct format for docking. However, after docking, all my ligands have this unusual bond formed which I am sure is not in the beginning pdb file of ligand. I only input within ring dihedral angle restraints at force constant = 400. Are these unusual bonds a cosnequence of high force constant?
It is most likely a visualization issue
I tried to submit it for Refinement and the bond is gone. So if it is only a visualization issue, is it okay to not do the refinement?
Did you try visualising it in a different viewer?