I was having this problem, and solved it.
Your 4 system files must be in the correct location - to avoid superuser issues this folder can be ~/.vice/C64
(for newbies, ~ means your home folder, and .vice will be invisible unless you display hidden files - Ctrl-H on Ubuntu - and you will need to create both .vice and C64 if you have a fresh VICE installation).
In that folder, you need just 4 files, with exactly the following names (case SeNsItIve):
1541
basic
chargen
kernal
(that's the disk drive, the Basic language, the Character Set and the main system "Kernal")
You can probably find these online somewhere.
You may need to rename the files from the names they have when you find them, note that they have NO suffix - not .rom, not .dat, just the names...
Once in place, running
x64 in a terminal should work, I saw a few errors but eventually it got there.
Hope this helps anyone who finds the Vice Manual a bit hard to fathom!