VMD

Installing MSMS for VMD

A great resource is the user manual [1].

One can run scripts in VMD command line (example scripts).

To run a script (in windows) type source in the command line followed by the fill name.

Useful atom selection commands:

"within <distance> of <selection>" 
"same <property> as <selection>"
same resid as within 5 of resname LIG

here is a script to calculate rmsd's: vmd.rmsd.csh.