You can use setCustomValidity function when oninvalid event occurs.

Like below:-

<input class="form-control" type="email" required="" 
    placeholder="username" oninvalid="this.setCustomValidity('Please Enter valid email')">
</input>

Update:-

To clear the message once you start entering use oninput="setCustomValidity('') attribute to clear the message.

<input class="form-control" type="email"  required="" placeholder="username"
 oninvalid="this.setCustomValidity('Please Enter valid email')"
 oninput="setCustomValidity('')"></input>