Hi Hari,
You do not need to input the password of root.
The process is the following:
1. use puttygen to generate ppk from pem, then you do not need to input the password with ppk
2. use putty to connect your instance with ppk
SAP HANA Developer Edition on Amazon Web Services (AWS)
Connect to Amazon EC2 with a private key using PuTTY and Pageant - TechRepublic
Best regards,
Wenjun