My 12th class subjects were physics, chemistry, maths, english, music, geospatial technology, while calculating my % can i skip maths and calculate it with my best 5 or not?
I'm sorry to inform you but you really can't do that. You must consider the 5 subjects that include mathematics, physics and chemistry. Along with these 3 you must consider a language subject. You've got freedom in selecting the last subject. You can select anything only here for the last slot.
So, you'll have to consider your mathematics marks here. You can't skip it while calculating your top 20 percentile.