Thank you for your quick response.
As u mentioned I have checked *.out file, MODFLOW did not get terminated successfully.
Last line of the output file is " SOLUTION DIDNOT CONVERGE FOR HEADS ".
While checking the simulation I have encountered with the error " Starting heads lower than bottom elevation" . I have solved that error by making IBOUND values inactive for those cells. Now there are no errors after I run "check simulation".
I used PCG solver, increased iterations to 100, 500 and 1000. But every time it ends up giving the same error.
Mapping of data (elevations, starting heads) to MODFLOW layers has been done correctly.
I am not able to understand where the error is there in my model.