Your query actually lacks most of the important facts pertinent to contracts of sale of immovable property. What were the terms of the Agreement with regard to payment; i.e.stages of part payment ... things like payment on execution of Agreement to Sell, at the time of registration fo Sale Deed, at handing over possession etc? Was there a forfeirure clause? There usually is one in Agreements to Sell. How did you end up registering a Sale Deed without having received the sale consideration? Are you sure its a Sale Deed or a registered Agreement to Sell?
Read this in totality with the terms and conditions of your Agreement to Sell and send a notice cancelling the Agreement to Sell. Keep the original dishonoured cheque and the original 'cheque return memo' with you in the event that the buyer files a Suit for Specific Performance in the future to compel you to perform the contract. It is one documentary evidence in support of the buyer's failure to perform his part of the bargain.
Sure, legally you can institute a complaint under Section 138 of the Negotiable Instruments Act but, as a matter of legal strategy and conventional usage, I'd strongly advice you against it. For one, under an Agreement to Sell, it is not the Seller's obligation to go seeking the consideration from a delinquent buyer. And secondly, and much more importantly, in instituting such a complaint, you'd only go on to create evidence by conduct reflecting that time was not of essence to the sale, which would be read in the favour of the buyer if in future he seeks to make payment after some delay stating that he is ready and willing to perform his part of the contract.
For the same reason, I'm also against a Suit for Specific Performance by you, the seller. If the buyer has failed to perform his contractual obligations, it is not for the seller to seek to compel the buyer to pay the full consideration in the event that neither the title nor possession has passed on or vested in the buyer (facts?).