Add this to ~/.latexmkrc:
~/.latexmkrc
add_cus_dep('acn', 'acr', 0, 'makeacn2acr'); sub makeacn2acr { system("makeindex -s \"$_[0].ist\" -t \"$_[0].alg\" -o \"$_[0].acr\" \"$_[0].acn\""); }