Hi Sheetal,
You should mention 'gratuity' entitlement in the appointment letter whether you follow CTC pattern or conventional pattern.
W.r.t. minimum service to be eligible for gratuity, it goes with your policy, whether your firm follow the Payment of Gratuity Act or similar one offered thru' other agencies like LIC etc. Under the PGAct, 5 yrs of 'continuous service' (4 yrs+240 days in the 5th yr.) is the criteria. However, if the service condition applicable is 'Fixed Term Employment' for a duration of <5 yrs service then gratuity is payable even if the qualifying service is <5 yrs.
W.r.t. 'deduction' towards gratuity, unless you really pay CTC there is no question of deduction arises. CTC, as I understand comprised of two parts, 1 is sum consists of basic, DA, HRA, other allowances, (bonus) which form part of monthly payable and 2nd part consists of components not payable monthly to employees such as EPF contribution, leave salary, gratuity etc which are payable not monthly but as and when due.