I did not since it wasn't mentioned in the tutorial. But in the nginx folder I see a two cert referencing iredmail certs. I think they are from the openssl that is installed originally?  Should I generate also new certs for nginx?  Any other thing I can check?  Thank you.

Yes, I followed the entire process to implement letsencrypt. The only thing is there is mention of sym link only for iredmail, but after running the installer, iredmail with openssl creates one for postgres and nginx too. Isn't that supposed to be changed too?  I am sorry for not clarifying, it's internal server error what I get.

Nothing.  nginx access log is normal, no error logs.  syslog looks normal t o me.  There is ClamAv doing the daily download, crons rnning some python scripts to clean db.
I could reinstall everything from scratch but what should I do to make letsencrypt work?  I have followed all of your tutorials. Any ideas?

Sure,
mx:~$ ls -l /etc/nginx/sites-enabled/
total 0
lrwxrwxrwx 1 root root 42 Jun  1 17:40 00-default.conf -> /etc/nginx/sites-available/00-default.conf
lrwxrwxrwx 1 root root 46 Jun  1 17:40 00-default-ssl.conf -> /etc/nginx/sites-available/00-default-ssl.conf

and,
mx: ~$ cat /etc/nginx/sites-enabled/00-default-ssl.conf
#
# Note: This file must be loaded before other virtual host config files,
#
# HTTPS
server {
    listen 443;
    server_name _;

    root /var/www/html;
    index index.php index.html;

    include /etc/nginx/templates/misc.tmpl;
    include /etc/nginx/templates/ssl.tmpl;
    include /etc/nginx/templates/iredadmin.tmpl;
    include /etc/nginx/templates/roundcube.tmpl;
    include /etc/nginx/templates/sogo.tmpl;
    include /etc/nginx/templates/netdata.tmpl;
    include /etc/nginx/templates/php-catchall.tmpl;
    include /etc/nginx/templates/stub_status.tmpl;
}

Thanks, here are the new ones.

mx:~$ cat /etc/nginx/templates/ssl.tmpl
ssl on;
ssl_protocols TLSv1.2;

# Fix 'The Logjam Attack'.
ssl_ciphers ECDH+AESGCM:DH+AESGCM:ECDH+AES256:DH+AES256:ECDH+AES128:DH+AES:ECDH+3DES:DH+3DES:RSA+AESGCM:RSA+AES:RSA+3DES:!aNULL:!MD5;
ssl_prefer_server_ciphers on;
ssl_dhparam /etc/ssl/dh2048_param.pem;

# To use your own ssl cert (e.g. LetsEncrypt), please create symbol link to
# ssl cert/key used below, so that we can manage this config file with Ansible.
#
# For example:
#
# rm -f /etc/ssl/private/iRedMail.key
# rm -f /etc/ssl/certs/iRedMail.crt
# ln -s /etc/letsencrypt/live/<domain>/privkey.pem /etc/ssl/private/iRedMail.key
# ln -s /etc/letsencrypt/live/<domain>/fullchain.pem /etc/ssl/certs/iRedMail.crt
#
ssl_certificate /etc/ssl/certs/iRedMail.crt;
ssl_certificate_key /etc/ssl/private/iRedMail.key;

and
mx:~$ ls -l /etc/letsencrypt/
total 32
drwx------ 4 root root 4096 Jun  1 18:18 accounts
drw-r--r-- 3 root root 4096 May 27 18:20 archive
-rw-r--r-- 1 root root  121 May 26  2018 cli.ini
drwxr-xr-x 2 root root 4096 May 27 18:20 csr
drwx------ 2 root root 4096 May 27 18:20 keys
drwxr-xr-x 3 root root 4096 May 27 18:20 live
drwxr-xr-x 2 root root 4096 May 27 18:20 renewal
drwxr-xr-x 5 root root 4096 May 27 18:17 renewal-hooks