Using VMRUN to shutdown Virtual Machines running with Virtual Server V2

I have successfully shutdown virtual machines running on VMServer V2 using the VMRUN command:

vmrun -T server -u username -p password -h https://10.55.11.11:8333/sdk stop "[standard]foldername\vmmachine.vmx" soft

On some Virtual Machines however I have applications running which will prompt for confirmation to be closed down.  Is there a way to close applications down elegantly. I would prefer not to use the 'hard' shutdown option in case it caused probles with the application.

Is there perhaps a way to answer all question with a Yes or an OK.

I would be grateful for any helpor suggestions.

Thanks in advance