You seem to mix up ispconfig 2 and ispconfig 3. ISPConfig 3 is a different software then ispconfig 2 and has different setup instructions. A script named 'setup' is part of ispconfig 2. So you have to download ispconfig 2 if the installation guide you used instructs you to run setup.
If you want to install ispconfig 3, you need a different setup. If the server ahs been configured for ispconfig 2, then you might have to format the server and reinstall it by using one of the following guides: