35) Autodock 4.0 (Installation and working)

Autodock 4.0 can be found from the following website,

http://mgltools.scripps.edu/downloads

download the software according to your computer appropriate operating system,

Installation:

I.windows installation:

1.Double click on to the MGLTools setup file.

2.Click "Next"

3.Accept the license agreement

4. Select your favorite destination folder to install the files and click 'Next"

5. wait for a while for the files to get installed

6. click on to the "Non commercial-Install all these packages"

7. click on to each package license

8. click "continue" button below

9. If you wish to launch shortcuts on your desktop , you can just click "finish"

10. And there your are ---- you can start working.

II. Linux installation:

NOTE: Autodock need to install from /root/, it can be installed from the /home/ directory itself.

1. Download MGLTools-1.5.2-Linux-x86-Install grant execute permission and run the installer.

To grant execute permission, type the following command at a command prompt: chmod +x MGLTools-1.5.2-Linux-x86-Install .

You can also use file manager to grant execute permission (right-click on the downloaded file and select Properties).

2) In the install wizard, click Next, select the destination and click Next again.

The default destination is /usr/local/MGLTools-1.5.2 for the root user and $HOME/MGLTools-1.5.2 for all others.

Please wait a few moments until the "License Agreements for add-on packages" window appears.

3) Complete the "License Agreements for add-on packages" form.

See Filling add-on packages license form for details.

4) Finally, click Finish to complete installation,

The README file contains detailed information on how to setup your environmental variables for command line usage.

Meanwhile download the following as well,

http://autodock.scripps.edu/downloads

click on the above link,

you will pop up with an registration form, kindly fill with necessary details and download the files which will be compatible to your operating system that your using.

This will contain 2 executable files,

1. autogrid

2.autodock.

NOTE: Make sure you install everything in the same destination folder including the 2 executable files

How to work on Autodock 4.0?

Here we go..!!

Follow the below steps,

*double click on to this icon

Your workspace will look like this,

,

Kindly use the pdb and ligand files which comes along with the installation of Autodock 4.0, will be present in (MGLTools/MGL ToolsPckgs/Pmv/doc). Use hsg1.pdb (protein) and ind.pdb (ligand)

Protein Preparation:   

File -  Read Molecule - Open the file.pdb. 

Select - Select from string - Type HOH* (to remove water molecules)

Edit -  Add  Polar only 

File - write PDB  save ur file in pdbfile.pdb extension just without changing the path.  just click and remove HETATM  Click sort nodes before saving .

Ligand Preparation:   

Ligand -   input  open ur ligand.pdb - just note down the summary of the ligand.  

Torsion tree -  choose root  

again go to torsion tree - detect root  

again go to torsion tree - show root expansion  

again go to torsion tree - choose torsions  just click ok  

again go to torison tree - set number of torsions  give the number of torisons that you get in the summary of the (TORSDOF) when u open the ligand. 

Output  Save the ligand file in the same directory in ligandfile.pdbqt   

Grid preparation:   

Select  select from string  just type your active site residues and then click ok   

Flexible residues - input macromolecule - choose macromolecule - click on your pdb from the panel displayed.  

Flexible residues - choose torsions from the currently selected residues - active site residues alone will be highlighted. 

Flexible residues - redisplay the macromolecule 

Flexible residues - save the files in both    flexible as (pdbfile_flex.pdbqt)   rigid as (pdbfile_rigid.pdbqt) .

Grid - macromolecule  - open- just open ur pdb_rigid.pdbqt file, ignore the warnings, if you have any metal ions in your  proteinn ,  just open ur grid file and u can find (0.00) for ur metal ions, just find the valency for them from net  and type maunally ther and again save it.you use this now. (if you dont hav metal ions), just ignore the warnings.  

set map types - choose ligand - click on ur ligand from the panel displayed  output - save in .gpf  edit gpf - dontt do anything just click ok for the time being 

Run -  run autogrid  just browse and locate ur autogrid.exe file , just browse and locate file .gpf (grid parameter file) and note that everything should be in the same directory, were you saved your pdb in protien preparation, dont change the path for your wish, just save were it is saving  just put your autodock.exe and autogrid.exe in the same directory were ur files has been saved  

Docking:  

Docking -  Macromolecule - set rigid file name - just again open ur pdb_rigid.pdbqt file  Ligand - choose ur ligand  search parameters- just delete one zero from the 2500000 (just make it to 4 zeros), otherwise it wil take very long time.  

Docking parameters- default  other option-autodock 4 parameters- default  output - save in ligandfile.dpf  

Edit DPF - just leave and click ok 

Run - run autock  just browse and locate ur autodock.exe file  just browse and locate file .dpf (dock parameter file) and then click ok.

Analysing the results:

open the widget "Analyse" and click open, locate the ligand.dlg file,

Next click on to Macromolecule found below Dockings, just click open, it will open by default, if you cannot able to view your protein properly, simply press "N" button from the keyboard.

To view your results click on to conformations -play,

It will open a widget shown in the picture.

click on to the ampersand (&) symbol.

Analyse your results..!!

NOTE: kindly save all your files in the same folder where you have been installed your MGLTools and executable files, if you want to run the programme from your favourite folder of your choice, make sure that you place just the executable files alone in the place were you have saved your all  files that you have been used during the course of working on Autodock, because without these executable files the programme wont run properly.       

For more details regarding the algorithm,f orcefields and interpretation of the data kindly go through the Autodock manual which is available at below mentioned web site, 

http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools