Hi all,
I have a query I completed docking with Auto dock vina in Windows machine. I want to visualize interaction (hydrogen) bonds between ligand and protein after docking with Auto dock vina. I used PHYMOL to visualize but i didnt get can you plz help me out in this regard.Plz suggest another visualize software.
You can use Accelrys DS visualizer. It is a free software.
Best Wishes
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.
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