Whenever i write help in the chat, it says the following (Error: Permissions manager is not accessable. Is the Permissionsex plugin enabled?) https://drive.google.com/open?id=0B1SZwZZ1QkWOQ3BwdGhlTUFxbWs (Permissions file)
Don't have access to view it. Instead, post your permissions.yml on http://pastebin.com/ and link the URL here
Nothing wrong with your permissions file, so its either due to doing /reload (which kills the permissionsEx and thus, the server commands - always restart, never /reload) or due to having the wrong Essentials version (since its essentials help that is giving the error)