I have joined two polypeptide chains by a peptide bond using cmd: BOND. I can save the modified molecule in a PSE file, but not a PDB file. When I reopen the PDB file, the newly formed peptide link is absent.
If you're doing this in PyMOL, it is likely because you're exporting only 1 object as the saved PDB. In older versions of PyMOL simply try 'save molecule' and cntrl-clicking (or shift-clicking) both objects when you save. This should combine them into a single file. In newer versions, 'export molecule' and change the selection to include both of the objects.
Hopefully this works and I'm not misunderstanding the issue. Good luck!