sub-domain installations

I have a wordpress installation on my main website. I’m a professor and I want to have separate installations of wordpress so I can have websites for my classes in sub-domains. For example, I have tried installing at arthistory2.mysite.com. The installation is there with no activated theme. when i try logging in it takes me to a page not found screen for mysite.com. How do I fix this? I thought I could do separate installations in different directories without them crossing over.