Add & improve documentation

[L30nardoSV]

Caveats:

1. https://github.com/ccsb-scripps/AutoDock-GPU/issues/20#issuecomment-502113557

It is possible that atom order in the reference ligand -xraylfile differs from atom order in the input ligand -lfile. If this is the case, and symmetry is turned off (-hsym 0), the RMSD will be calculated incorrectly. We may want to add this to the documentation.

2. https://github.com/ccsb-scripps/AutoDock-GPU/issues/20#issuecomment-502113557

Add -xraylfile information into README