the_permalink() not working in a root installation

Question

I hope someone can help me. I have a root installation of WP, but not as index.php (it's actually news.php). Consequently the_permalink() doesn't work, as the root of the website is a different page.

Is there any way I can fix this? Perhaps something in the .htaccess that detects ? in the URL and redirects to news.php/? etc.

Thanks for any assistance, I'm a newb at WP!