Hello, I've deleted user root through phpmyadmin and now when I type mysql in prompt it gives me error 1045 (280000).
I tried to start with grant table option but it prompt out a lot of messages regarding so libraries.
What can I do now ?

Thank you

Back up your database. Proceed slowly and research restoring. It's been a while since I've done this but I was able to restore my tables.
Research, backup. Can you login from tty?
logout
cwc@azzerare ~ $ mysql -u root -p
Enter password:
Welcome to the MySQL monitor. Commands end with ; or \g.
Your MySQL connection id is 271
Server version: 5.1.70-log Gentoo Linux mysql-5.1.70

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Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql>

Do you mean the "skip-grant-tables" option?

https://www.google.com/#q=reset+root+mysql+password

usually mysql creates some more root users, and guest-users without username, though they are not granted sufficient rights to manage the mysql server. So you should stop the server and restore the whole mysql directory in your datadir from backup. Before that you may want to copy the old directory to e.g. mysqlold within the datadir. Once yo get the server started again, you'll find that as a separate database and can copy entries, that may be missing in your backup.