I'm on to configuring smeserver to enable ldap authentication via php ...
I don't know exactly what you mean by that. You seem to say you are writing some php code to re-configure smeserver with ldap authentication enabled. But that seems unlikely...
ldap protocol worked fine though but I prefer the more secure ldaps
OK. And I guess from the subject, somewhere you are seeing "Peer's Certificate issuer is not recognized". Presumably you have an ldaps client somewhere which doesn't like smeserver's self-signed certificate.
But then you mention AD, so perhaps you mean something else. Maybe you should explain in more detail.
I just need some help on which files should I touch and what other commands should I trigger to add our active directory certificate as trusted ca in smeserver box.
Why do you think that would help? You probably have to look through openssl and openldap documentation to work that stuff out.