innodb.php

<?php

// your connection
mysql_connect("localhost","root","root");
mysql_select_db("d6");

// convert
$result = mysql_query("SHOW TABLES");
while ($row = mysql_fetch_array($result)) {
  foreach ($row as $key => $table) {
    $query = "ALTER TABLE " . $table . " ENGINE=InnoDB;";
    mysql_query($query);
  }
}