Visualizing PDB file in VMD, how to upload molecules?
I found a shortcut, and that is if I go to (click on):


file
New Molecule
Enter in the "browser" window the direct PDB accession code "3WD5" (for my protein) then VMD retrieved the protein structure form the PDB database on its own, and is showing it as it should in the visualization window. 


However, this does still not resolve why it will not load a downloaded PDB file, but I suspect its most likely due to some problem with downloading of the files or installing the program its self that has gone wrong.