What aspect of 'nano-scale' are you trying to capture? If its just the size then thats easy as Abaqus does not have a fixed size scale. I've modelled metals at the micro-scale using Abaqus, using crystal plasticity theory to represent the effects of atomic slip. Never nano-scale though. Would you have to model individual atomic interactions?
In my opinion, continuum FE formulations are not very useful at nano-scale. However, if you are interested in modeling inter-atomic interactions using user-defined "structural-like" elements you might be interested in the user subroutine UEL.
I think currently researchers are interested in multi-scale simulations where continuum FE formulations are coupled with molecular dynamics approaches.