As per EPF definition, the PF contribution is calculated on Basic + VDA, with a PF Salary Limit up to 6500/-. Therefore, you have to deduct the PF Contribution on Rs. 6000/- (Basic + VDA). If the verification of the amount Rs. 6000/- is broken down into Basic, DA, and other allowances like HRA, CCA, for example, Basic Rs. 4000 + VDA Rs.1000 + HRA Rs.1000/-, then you have to deduct the PF contribution on Rs. 5000/-, not on 6000/-.
According to the Minimum Wages Act, the total remuneration should not be less than the fixed minimum rate.