I am sorry but i am not getting your point. you have the molecule and want to dock it but don't know about the protein of interest? that seems like you have the solution and trying to find the question. please specify what you want to do. i think i am not getting it from your question.
I tried tarfisdock server. I tried to upload my file in tarfisdock server. But the website shows that "You have submitted a valid Mol2 file!FTP connection has failed!". how can I solve this problem