Calculating entropy is difficult, and you typically can only calculate it up to a constant. The most straight-forward way is to run *many* NVE simulations at varying E, calculate T in each one, then integrate 1/T(E) to get S(E)+C.
Can someone please provide me a sample input script to calculate the entropy of a system?
There is no command or input script for this. Of course there are all sorts of other free energy calculation methods that would also get you the entropy, but I'd suggest you look into the basics of molecular simulation before tackling those techniques.