How to update mysql my.cnf without getting error?
You mentioned these four options

innodb_buffer_pool_size
innodb_additional_mem_pool_size
innodb_log_file_size
innodb_log_buffer_size


The one that worries me is innodb_log_file_size

Upon initial startup, innodb_log_file_size is 5MB. You need to make new InnoDB log files. There are two InnoDB log files that got created 5MB each:


/var/lib/mysql/ib_logfile0
/var/lib/mysql/ib_logfile1


All you have to do is the following:

service mysql stop
rm -f ib_logfile*
service mysql start


The two log files will be regenerated as 1GB files. I wrote about this last year.

Give it a Try !!!

BTW DO NOT TOUCH /var/lib/mysql/ibata1 !!!