The challenge returns a 404 when curling from various vantage points. I receive 200 OK’s when running curl -IL http://idp.unishivaji.ac.in/.well-known/acme-challenge/
@Vaishali, could you try using a client such as certbot or acme.sh since you have root access to the server? Certbot can be found at https://certbot.eff.org/ and acme.sh at https://github.com/Neilpang/acme.sh
On an apache server I run, this is how I issue/renew certificates.
certbot certonly \
--webroot \
--webroot-path /path/to/htdocs \
--renew-by-default \
--email $YOUREMAIL \
--text \
--agree-tos \
-d idp.unishivaji.ac.in
Additionally, could you post your vhost configuration for that site?