Hi,

You should save your complex as PDB in ADT,

and open it in UCSF Chimera.

https://www.cgl.ucsf.edu/chimera/

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

Chimera can display amino acid names placing the mouse cursor over an amino acids.

https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html

Hi again,

In ADT,

To display all amino acid names,

click on Display -> Label -> by Properties -> Residue -> name -> OK,

To unlabel them,

click on Display -> Label -> by Properties -> unlabel -> Residue -> name -> OK,

To display the names of the selected amino acids,

click an atom of an amino acid with shift key ->  Display -> Label -> by Properties -> Residue -> name -> OK.

Hii Yoshinobu,

Thank you so much for your input..it helped me...

I'm having the same probem!

Great Yoshinobu Ishikawa for your input!

I will try!

Hi,

You can also visulalize your map of protein-ligand interactions in Pymol. First, load your receptor in PDB format and then load the dlg file.

You can also use Ligplot+ its also simple and quite descriptive as well. Along with that, chimera, discovery studio are other visualization tools, each having its own benefits and specificity, depending upon user's needs.

I dont know if you have already found the solution or not, but if not, here you go:

If you want to visualise it in Autodock only, use AutoDockTools GUI. Go to

Analysis -> Dockings -> Open (select your dlg file).

Next, (its better to keep your pdbqt file of receptor in the same directory as dlg file)

Analysis -> Dockings -> Macromolecules -> Open

(If not in the same directory, File-> Read Molecule (select your pdbqt file wherever it is; then, Analysis -> Dockings -> Macromolecules -> Choose (select your pdbqt file))

Next,

Analysis -> Conformation -> Play, ranked by energy (first is supposed to be having least energy i.e. highest binding energy)

Finally,

Analysis -> Dockings -> Show Interactions

So, now you should be able to see interacting residues of receptor, and also can save a picture also.

Let me know if you face any problem.