What is the relevance of "deducting" gratuity amount from the CTC? The CTC itself is wrong. You should take the salary out of it and see if there is any deduction by way of gratuity. There will not be any deduction towards gratuity.
Now coming to the point of discussion, every employer is expected to create/ provide for a gratuity fund as per the Accounting Standards. Your Accountant will not finalise your Profit and Loss account and Balance sheet without providing for gratuity liability and that provision will be made after an actuarial valuation. This is done by taking in to account the age of employees, their retirement date, probable number of employees who are expected to leave the company in the next year etc. By making this provision, the company will be able to pay gratuity without depleting their working capital.
If your state has not made it mandatory to invest the said fund with LIC, then you can keep it as such under a separate trust fund.