actually in my system i have terminal alkyne group and free acid groups , I want to couple with primary amine of amino acid in HBTU condition without disturbing terminal alkyne.
You should be fine for this type of coupling chemistry. Don't use an enormous excess of base and make sure you have no trace metals present (pre-rinse your glassware with acid before regular cleaning).
As an added precaution, don't expose your reaction to atmosphere while in progress.
Actually the triple bond will not be influenced of presence of base. But addition reactions are catalyzed with metal (especially mercury) ions. Nitrogen atmosphere also be useful.