Hello,

Yes, you can do that by giving the initial deposit an only appear for government colleges and central universities in the first round. Later on you could apply for Deemed universities after paying amount of 2lakhs in the second round. Counselling for government and central colleges are conducted by MCC and for deemed universities it is conducted by DGHS on behalf of MCC so both are separate and there is no issue in apply for both.

Hope it helps.

Good luck.