You probably want to fix your SEP with respect to other atoms it is docked against, correct? If so, then the easy thing to do is generate pairwise distances between the SEP atom(s) of interest, and the atoms that those atoms contact. Then just make a list of AtomPair constraints as the documentation you’ve already read suggests.
If that’s not what you wanted to do, can you describe it more specifically?
Thanks for the kind suggestions.This is exactly what I want.
I will try use SEP in my docking process although the program does not recognize it. And add restrains of between SEP atoms and the near by residues to avoid disruption of the peptide backbone. Hopefully it will work.