Is the error reproducible? Try running the script again and see if it reappears.
Is a file called "Au-molecular-Au.vnl" produced at all? Do you have write privileges in the directory where it's supposed to go? If running via a queue, this may not be the case as the local directory under execution can be a system directory. For this reason, always use a full absolute path name to the VNL file (like, /home/username/calcs/myfile.vnl), which of course should be a valid path on the system, accessible from each node on the cluster.
Also, see if you can run this simple test script in parallel without errors:
from ATK.KohnSham import *
from ATK.MPI import processIsMaster
if processIsMaster(): file = VNLFile('test.vnl')
if processIsMaster():
print 'Master node'
elements = [Hydrogen, Hydrogen]
coordinates = [[ 0. , 0. , -0.36999989],
[ 0. , 0. , 0.36999989]]*Angstrom
molecule_configuration = MoleculeConfiguration(elements,coordinates)
if processIsMaster(): file.addToSample(molecule_configuration, 'molecule_configuration')
Check in particular if the text "Master node" is written to the terminal (stdout) only once.
If it is printed twice (when running on two nodes), you have a problem in your parallel setup (typically, this appears when not using MPICH2 as the parallelization library) which will prevent you from running ATK in parallel properly anyway, so you need to address and fix this issue (by installing MPICH2, in case you haven't).