You cannot expect to parse a date with a SimpleDateFormat that is set up with a different format.
To parse your “Thu Jun 18 20:56:02 EDT 2009” date string you need a SimpleDateFormat like this (roughly):
SimpleDateFormat parser=new SimpleDateFormat("EEE MMM d HH:mm:ss zzz yyyy");
Use this to parse the string into a Date, and then your other SimpleDateFormat to turn that Date into the format you want.
String input = "Thu Jun 18 20:56:02 EDT 2009";
SimpleDateFormat parser = new SimpleDateFormat("EEE MMM d HH:mm:ss zzz yyyy");
Date date = parser.parse(input);
SimpleDateFormat formatter = new SimpleDateFormat("yyyy-MM-dd");
String formattedDate = formatter.format(date);
...
JavaDoc: http://docs.oracle.com/javase/7/docs/api/java/text/SimpleDateFormat.html