The conf file needs to be in ~/root/.yacoin/yacoin.conf
That is, if you login as root.
it has to be in ~/.yacoin/yacoin.conf
read
http://www.yacoin.org/I always login as root so the home dir is /root/
however you are loged in, the yacoin wallet folder is always ~/.yacoin/
The "~" specifies your home folder. If you loged in as root, ~ will be /root, if you loged in as say, kalgecin, ~ would be /home/kalgecin