InnoDB to MyISAM Conversion Problem

Question

I have a dedicated server based on CentOS 5 OS , mysql 5 and phpmyadmin

I was trying to convert all database tables from InnoDB to MYISAM. I tried to do it by setting in /etc/my.cnf file the value

skip-innodb 

Afterwards, I found some errors in some php scripts in the server

Unknown table engine 'InnoDB'

I checked some databases in phpmyadmin i found in each database some tables IN USE

How can I make a successful conversion of all tables from InnoDB to MyISAM ?