We need some clarification. Is the pentamer you speak of a peptide made of five amino acids? If not that, then please specify.
If you want to attach a glycan to a single, zwitterionic, amino acid, GLYCAM has, available for this purpose, variants of serine and threonine (residue names ZOLS and ZOLT). If you want to model any other amino acids, or if you don't want the zwitterionic form, you will need to generate a residue with partial atomic charges.
Our server will only detect that two cysteine residues are capable of forming a disulfide bond if their sulfur atoms are proximal. For this to happen, your peptide will need to be uploaded in a conformation where that is the case.
If none of what I just said answers your questions, then I didn't understand your situation.