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I've created a domain.csr and domain.key with this code:

openssl req -new -newkey rsa:2048 -nodes -keyout domain.key -out domain.csr

Then, using these two I bought a certificate and I got certificate from RapidSSL.

RapidSSL gave me a my_domain.crt. Everything is fine.

However, when I try to install this .crt file, there is a problem.

Documentation says that:

Concatenate the SSL and Intermediate CA Certificate using this code:

cat intermediateCA.crt >> SSL_Certificate.crt

But I don't have any kind of .crt file in my remote server, and also I don't know which one is mine which I gave: intermediateCA.crt or SSL_Certificate.crt

How can I install this certificate on my web server?

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my_domain.crt is your SSL certificate, and you can download the intermediate certificate from the provider's website here. It's probably this one; you need to copy the text including -----BEGIN CERTIFICATE----- and -----END CERTIFICATE-----, and save it on your server as intermediate_CA.crt. The names of the certificate files don't really matter.

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