The default terminal patches for nucleic acids are NONE, which is not OK. You have to specify whether you want a charged (-1) phosphate (5PHO, 3PHO) or a non-charged hydroxyl (5TER, 3TER) at either end; both exist in nature, so the user has to make the decision, and that is also why there is no default patch. One often wants to avoid having many charges so 5TER and 3TER are commonly used. In your case the phoshpate might be more appropriate. It is also quite easy to model a couple of missing nucleotides at the end.
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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden