Hi all

I have successfully docked ligands into protein and obtained potential hits. From DS, some hydrogen bond interactions are formed between my ligand and protein. Upon converting the complex into pdb file and viewing this interaction in pymol, I observe either the hydrogen bonds viewed in DS are not available or different hydrogen bond contacts with different residues are shown in pymol. Why the difference? Can anyone help with the best way to prepare the protein-ligand complex in DS and to view the same interactions in pymol, if possible?