Hello abhishek.kumar@chassisbrakes.com,
We provide, together with our toolbox in the following path NXP_MBDToolbox_MPC57xx\code\tools\ClockConfig\mbdt_default_clock_config_panther, an S32DSforPA project that describes the clock configuration used in the MBDT Toolbox. You can import that project in the S32DS and modify the project clock configuration in PEX according to your needs.
Once you generate the code, in the clockMan1.c you will find a clock_manager_user_config_t structure. This one contains the clock configuration that must be replaced in our toolbox.

So you need to copy the generated clock configuration in the clock_manager_user_config_t clockMan1_InitConfig0_panther structure in the NXP_MBDToolbox_MPC57xx\code\mbdtbx_mpc574x\src\c_library\mpc_clock_man_panther.c. Together with that, you will need to change, in the new configuration, the count and peripherals field, as in the following screenshoot:

I recommend you to backup the initial mpc_clock_man_panther.c.
Hope this helps,
Marius