I want to store my app's databases on my own server.
Right now, I'm storing it on parse.com server.
Is there any way to move the databases to my own server and still get access to it using parse.com SDK?
No Parse SDK will not allow that. For one obvious example, you cannot configure location for PFFile to be stored. You may consider opting for storing references to URLs rather than PFFiles in your Parse objects. However, I think there's still some issue with Parse SDK not allowing you to download multiple resources with a single method call.