ADL: regarding result analysis of autodock Vina

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ADL: regarding result analysis of autodock Vina

Neha lohia
Dear All

I am facing difficulty in analyzing the results of autodock Vina. How can i
visualize  the interaction between the ligand and the receptor.

--
Regards
Neha Lohia
Research Scholar
C/O Dr. Manoj Baranwal
Assistant Professor
Dept of Biotechnology
Thapar University
Patiala, Punjab
________________________________________________
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Re: ADL: regarding result analysis of autodock Vina

Ruth Huey
Hi,
You can analyze AutoDock Vina results in AutoDockTools (ADT).
First start ADT then follow these steps:

1. Analyze->Dockings->Open AutoDock vina Result...
   In 'AutoDock Vina Result File:' browser widget locate + select your vina result
     eg ind_vina.pdbqt
   Then click Open

    In the "Load MODELS as:" widget which will open, use the option 'Single molecule with multiple conformations' and click OK

    'AD41analyze_readVinaResult WARNING" message opens displaying the number of available docked conformations found in the vina file. Click OK to close 'AD41_readVinaResult'

At this point the docked molecule is displayed in the lowest energy conformation.
You can use the keyboard left + right arrow keys to step through the other docked conformations vina found.
     
2. Analyze->Macromolecule->Open...
   In 'AutoDock Vina Receptor File:' browser widget locate + select your receptor pdbqt file
     eg hsg1.pdbqt
   Then click Open

3. Analyze->Dockings->Show Interactions
This  changes display. By default it shows:
   1. molecular surface for ligand with colored by (1) atom type for ligand atoms close to receptor atoms
      and (2) white for ligand atoms not close to any receptor atoms
   2. wire spheres around receptor atoms close to a ligand atom [colored by receptor atom type]
   3. labels + sticks for residues close to ligand
   Activating hydrogen bonds option adds wire spheres around hydrogen-bonding atoms AND opens
  'Show Hydrogen Bonds as Spheres' widget showing each hydrogen bond as green spheres with adjustable spacing + radii.
  Clicking on entries in this widget, eg "ind_vina:I:IND201:H21 1", toggle their visibility in ADT.

AND it opens 'Binding Site Interactions display options' widget with these options:
    1. update display for each conformation  <on by default>
    2. set background color <customizable>
    3. display msms for current docked conformation of ligand
    4. display spheres either as wireframe or solid  
    5. display spheres on atoms in close contact
    6. display spheres on atoms in hydrogen bonds
    7. display secondary structure ribbon for receptor residues near ligand atoms
    8. display secondary structure ribbon for all other receptor residues
    9. display labels on receptor residues near ligand atoms
   10. output list of:
       -ligand contacts
       -receptor contacts
       -hydrogen bonds
       NB: selecting one of these results in printing its information in the  *Python Shell*
       [which is opened with white-square labelled button in center of second row at the top of ADT GUI]
   11. display pi-pi interactions: checks for both pi-pi interactions and t_shaped interactions
   12. display pi-cation interactions: checks for cation_pi, pi_cation (and pi-pi) interactions

   Pressing the 'Save Image' can be used to capture current content of DejaVu Camera
   1. FIRST increase the picture quality:
         open the 'SetAntialiasing' widget:
            3D Graphics->SetAntialiasing  
         Click on 15
   2. Click 'Save Image' button in Binding Site Interactions display options widget
   3. Type in a file name for the Output File: in the SaveImage widget
          eg VinaModel4.png
   4. Click OK
   5. Restore Antialiasing value to 0 in 'SetAntialiasing' widget and click 'DISMISS'.

      Best wishes,
        Ruth
________________________________________
From: [hidden email] [[hidden email]] On Behalf Of Neha lohia [[hidden email]]
Sent: Friday, April 11, 2014 5:58 AM
To: [hidden email]
Subject: ADL: regarding result analysis of autodock Vina

Dear All

I am facing difficulty in analyzing the results of autodock Vina. How can i
visualize  the interaction between the ligand and the receptor.

--
Regards
Neha Lohia
Research Scholar
C/O Dr. Manoj Baranwal
Assistant Professor
Dept of Biotechnology
Thapar University
Patiala, Punjab
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---