Hello,
Yes, you can register for bams councelling even without registering for any other councelling. The admission to any college will be done strictly on the basis of neet score . Only candidates, who have qualified the neet exam will be allowed to participate in the councelling process  for the ayush courses.
There are around 36, 000 seats available under the AYUSH colleges for the various UG courses currently.
Just make sure that you keep yourself updated about all the councelling related details.
Good luck

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