Catalyzes the transfer of diphosphate from ATP to 6-hydroxymethyl-7,8-dihydropterin (6-HMD), leading to 6-hydroxymethyl-7,8-dihydropterin diphosphate (6-HMDP). To a lesser extent, can also use CTP, UTP, and GTP as the nucleotide triphosphate substrate. 6-hydroxymethyl-7,8-dihydropterin + ATP = (7,8-dihydropterin-6-yl)methyl diphosphate + AMP + H(+) Belongs to the archaeal 6-HMPDK family.