Hi Anil,
A quick answer is you maynot get ZCL groups/scenes support by using an AP to work with a ZNP which loads the default stack firmware. The reason is groups cluster depends on APS groups features and currently these functions (as the error you have got indicates) are not exposed via ZNP interface.
Here in your application, Linux (on a PC or Embedded platform) plays as an AP. You have to expand the ZNP serial interface commands by exposing the lost groups access APIs(such as aps_FindGroup) in ZNP side and then make a proxy function in AP side to support ZCL groups cluster.
Check this post raised by me which describes the same issue as you.
http://e2e.ti.com/support/low_power_rf/f/158/p/227094/799458.aspx#799458
