Swaroopa,
You may also need to create/define your database globals if you are using SDML database tags in your queries. For example <<database.getSystemTime>> will evaluate differently for MySQL compared to SqlServer or Oracle
You will want to create a mysql_sd.ini file containing the various database SDML tags and their corresponding MySql values. I would suggest copying the sqlserver_sd.ini and then update based on mysql syntax.
You will then want to update your Agentry.ini queryConstantFiles entry for the mySql backend settings to point to your new filename.
--Bill