This is highly dependent upon which VPN is used. Most of them use some defined port number to pass their traffic, but it is different for every vendor. You will need to consult with the chosen vendor for the proper port information. On the other hand, if the only way the server is to be reached is via VPN, why not put the VPN box in parallel with the firewall? Let VPN traffic go to the VPN box and on to the server, and all other traffic go to the firewall and the machines behind it. That is a very common architecture.
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