The Molecular Graphics Laboratory Forum

Hi everybody
I'm new in this forum.I've just begun studying docking and mere novice in this field.So I have a few question.Firstly,in a typical docking study which route should i follow.I see that there are many programs used in a docking process such as MGL Tools,Auto Dock Vina,Auto Ligand,PyRx,Raccoon and so on,so I am a little confused in which turn i should use these.I am not sure but it seems to me that first i should use Auto Ligand to predict binding side.As i think,should i begin with Auto Ligand? If not,with which one?

Many Thanks in advance

If you are in the right forum, and you want to use Vina, then the tutorial video is pretty much self-explicative. The pathway is very straight forward in most of the cases. You open your receptor in ADT, erase the water, add the hydrogens, merge the non-polar ones, and assign it as the receptor in the grid->macromolecule->choose option. This will add the geisteiger charges to the receptor. For the ligand the pathway is pretty much the same, but using exclusively the Ligand tab to do it. The files saved as pdbqt can be used by vina if you give the program the right parameters.
The other programs you mention over there are not necesarily used (PyRx and Racoon are used for screening; Auto Ligand was used to find the binding pocket for AD4). Just follow the instructions from the tutorial.

Thank You so much