I wanted to make a 4pin rgb header output form motherboard converted to 3pin rgb header by arduino like
DEEPCOOL RGB Convertor, 5V ADD-RGB to 12V RGB Transfer Hub, which convert the 4pin rgb header on motherboard to 3 pin rgb header. I have started using the arduino since a month so i don't know much about this can any one help me with this
What is the pinout from the 4 pin header?
Sorry, this is clearly way beyond your league! 
Too much of a "niche" product for most of us here either. 
That depends, look in the manual for your motherboard, and if you do not have one you can download it from the manufacturer. When you get it working post your schematic because from where I am we need a common plus the three colors, diode orientation determines the polarity. I would to a bit of research on basic electronics and this will then make this easier to understand.
See #2! 
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