You can use Accelrys DS visualizer. It is a free software.

Best Wishes

You can use UCSF Chimera software, from the follwing link. It has a option for viewing result of autodock vina.

http://www.cgl.ucsf.edu/chimera/download.html

Hi,

To visualize your protein-ligand interaction, you can also use PoseView

http://poseview.zbh.uni-hamburg.de/

And also LigPlot Plus

http://www.ebi.ac.uk/thornton-srv/software/LigPlus/

Hi,

You should use UCSF Chimera and OpenBabel.

http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html

http://openbabel.org/docs/2.3.1/GUI/GUI.html

First, you should convert vina_ligand.out to vina_ligand.mol2 by using OpenBabel.

Second, in Chimera,

Select -> open -> receptor.pdbqt -> Type selection -> PDB

Actions -> Atoms/Bonds -> show

Actions -> Ribbon -> hide

Tools -> Surface/Binding Analysis -> ViewDock -> File type -> GOLD -> vina_ligand.mol2

Finally,

Tools -> Structure Analysis -> FindHBond -> Find theses bonds -> inter-model

Hydrogen bonds will be shown.

To calculate distance between two atoms,

Tools -> Structure Analysis -> Distances,

click first atom with control key, 

then, click second atom with control and shift keys,

After selecting two atoms, click "create" button in the structure measurements panel.

To clear selection, click anywhere with control key.

After you write the protein-ligand complex as a .pdb file, you can use Maestro (Schrodinger) or LigPlot+ for for studying protein-ligand interactions.