Dear   Tehreem

I hope this comment finds you in good health and spirit.

For running ADT, you should be following next steps:

1- Make sure that if python 2.5 installed on your PC: you can download it from the following URL:

https://www.python.org/download/releases/2.5/

2- install Autodock tools: you can download it at:

http://autodock.scripps.edu/downloads/autodock-4-2-x-installation-on-windows/

3- install mgltools:

http://mgltools.scripps.edu/downloads

After having finished installation of above tools, you can run ADT. Here, I recommend you to following my current protocol for running it:

1- create a workfolder for your job and tag it based on your favorite name. (e.g. project)

2- running ADT in start menu in windows:

after running you should set its directory: following these steps:

a) open ADT> File> Preferences>set> Startup Directory (in this section you should put on your workfolder path and set it). for example: “C:\Users\project

3- prepare ligand and protein in ".pdb" format. Notice, you must labeled them by "Ligand" and "Protein" keywords.

after having finished these steps you can run ADT: Well! you should do the below ways:

1- open ADT:

File > Read Molecule> Select Protein File (“.pdb” file)

Then:

Edit > Hydrogens >Add>>>>>> Polar Only >OK

Edit > Hydrogens> Merge Non Polar >  Continue (in this step if you see any warning please click on "continue")

then:

Edit > Charges > Add Kolman Charges> Ok

File > Save > Write PDB> >Sort Nodes (Check) > OK > (Overwrite) YES

Well! in the next step you should try prepare the ligand:

Ligand > Input > Open> Select Ligand File (“.pdb” file) > OK

Now repeat above steps and then: (in this section you must add charge to your ligand. So, click on Edit menu and:

Edite> Charges> compute Gasteiger

Ligand > Output > Save as PDBQT

******************************

Now you should be executing AutoGrid4:

For run AutoGrid following the below steps:

1-Grid > Macromole > Choose>  Click (Protein) > Select Molecule > OK > save

2-Grid> Set Map types >Choose Ligand> Click (Ligand) > Select Ligand

3-Grid > GridBox> Set the BOX> File > Close Saving Current

4-Grid > Output > Save GPF> grid.gpf> save

5-Run > Run AutoGrid:

a) Select Program Pathname: ‘autogrid4.exe’ (i.e. C:\Program Files (x86) \The Scripps Research Institute\Autodock\4.2.6)

b) Select Parameter Filename: ‘grid.gpf’ (you should select it based on your workfolder path)

c) Launch!

Notice! in this step you must waiting for ADT response. please don't "dismiss" it!

***************************************************************

After having finished above steps following the below ways:

Run ADT:

1)Docking > Macromolecule > Set Rigid filename> Select ‘Protein.pdbqt’ > Open

2-Docking > Ligand > Choose> Click ‘Ligand’ > Select Ligand> Accept

3-Docking > Search Parameters > Genetic Algorithm> Accept

4-Docking > Output > Lamarckian GA> Save file as ‘dock.dpf’

5-Run > Run AutoDock 

A) Select Program Pathname: ‘autodock4.exe’ (C:\Program Files (x86)\The Scripps Research Institute\Autodock\4.2.6)

B) Select Parameter Filename: ‘dock.dpf’ (Based on you workfolder path)

C) Launch!

Please wait for finishing and don't dismiss it!!

***********************************************************

Docking result analysis:

1-Analyze > Docking > Open> Select ‘dock.dlg’ > Open >Assign Ligand New Name > OK

2-Analyze > Macromolecule > Choose> Click ‘Protein’ > Select Macromolecule

3- Analyze > Conformations> Play, Ranked By Energy > Click on the ‘&’ Button

4-Set Play Options >Check ‘Build H-Bonds’> View the hydrogen bonds formed > Check ‘Show Info’> View the Interaction Energy > Build Current Write Complex> Save as ‘Result.pdb’ ” Save....

Now you can see all of your docking results!

This current protocol can help you for running ADT. I hope it was useful for you. Please do not hesitate to contact me if you have any further questions. Otherwise, I hope that we can work together successfully again another time.

All the best,

Hassan

Hi Sana,

You can also use babel to create receptor pdbqt file.

http://mvirdb1.llnl.gov/static_catsid/vina/usersGuide.html

http://openbabel.org/wiki/Category:Installation

hi,

Import your file in pdb format to software then click on file and save with pdbqt format.

Thanks Yoshinobu Ishikawa and Mokhtar Nosrati

Dear   Tehreem

I hope this comment finds you in good health and spirit.

For running ADT, you should be following next steps:

1- Make sure that if python 2.5 installed on your PC: you can download it from the following URL:

https://www.python.org/download/releases/2.5/

2- install Autodock tools: you can download it at:

http://autodock.scripps.edu/downloads/autodock-4-2-x-installation-on-windows/

3- install mgltools:

http://mgltools.scripps.edu/downloads

After having finished installation of above tools, you can run ADT. Here, I recommend you to following my current protocol for running it:

1- create a workfolder for your job and tag it based on your favorite name. (e.g. project)

2- running ADT in start menu in windows:

after running you should set its directory: following these steps:

a) open ADT> File> Preferences>set> Startup Directory (in this section you should put on your workfolder path and set it). for example: “C:\Users\project

3- prepare ligand and protein in ".pdb" format. Notice, you must labeled them by "Ligand" and "Protein" keywords.

after having finished these steps you can run ADT: Well! you should do the below ways:

1- open ADT:

File > Read Molecule> Select Protein File (“.pdb” file)

Then:

Edit > Hydrogens >Add>>>>>> Polar Only >OK

Edit > Hydrogens> Merge Non Polar >  Continue (in this step if you see any warning please click on "continue")

then:

Edit > Charges > Add Kolman Charges> Ok

File > Save > Write PDB> >Sort Nodes (Check) > OK > (Overwrite) YES

Well! in the next step you should try prepare the ligand:

Ligand > Input > Open> Select Ligand File (“.pdb” file) > OK

Now repeat above steps and then: (in this section you must add charge to your ligand. So, click on Edit menu and:

Edite> Charges> compute Gasteiger

Ligand > Output > Save as PDBQT

******************************

Now you should be executing AutoGrid4:

For run AutoGrid following the below steps:

1-Grid > Macromole > Choose>  Click (Protein) > Select Molecule > OK > save

2-Grid> Set Map types >Choose Ligand> Click (Ligand) > Select Ligand

3-Grid > GridBox> Set the BOX> File > Close Saving Current

4-Grid > Output > Save GPF> grid.gpf> save

5-Run > Run AutoGrid:

a) Select Program Pathname: ‘autogrid4.exe’ (i.e. C:\Program Files (x86) \The Scripps Research Institute\Autodock\4.2.6)

b) Select Parameter Filename: ‘grid.gpf’ (you should select it based on your workfolder path)

c) Launch!

Notice! in this step you must waiting for ADT response. please don't "dismiss" it!

***************************************************************

After having finished above steps following the below ways:

Run ADT:

1)Docking > Macromolecule > Set Rigid filename> Select ‘Protein.pdbqt’ > Open

2-Docking > Ligand > Choose> Click ‘Ligand’ > Select Ligand> Accept

3-Docking > Search Parameters > Genetic Algorithm> Accept

4-Docking > Output > Lamarckian GA> Save file as ‘dock.dpf’

5-Run > Run AutoDock 

A) Select Program Pathname: ‘autodock4.exe’ (C:\Program Files (x86)\The Scripps Research Institute\Autodock\4.2.6)

B) Select Parameter Filename: ‘dock.dpf’ (Based on you workfolder path)

C) Launch!

Please wait for finishing and don't dismiss it!!

***********************************************************

Docking result analysis:

1-Analyze > Docking > Open> Select ‘dock.dlg’ > Open >Assign Ligand New Name > OK

2-Analyze > Macromolecule > Choose> Click ‘Protein’ > Select Macromolecule

3- Analyze > Conformations> Play, Ranked By Energy > Click on the ‘&’ Button

4-Set Play Options >Check ‘Build H-Bonds’> View the hydrogen bonds formed > Check ‘Show Info’> View the Interaction Energy > Build Current Write Complex> Save as ‘Result.pdb’ ” Save....

Now you can see all of your docking results!

This current protocol can help you for running ADT. I hope it was useful for you. Please do not hesitate to contact me if you have any further questions. Otherwise, I hope that we can work together successfully again another time.

All the best,

Hassan

Thanks Hassan 

I'll follow these steps . 

Dear Tehreem

If you have any problem with ADT please touch me directly.

[email protected]

I'm at your service for any help.

May be helpful to someone else. worked for me.

1. Load Receptor: File -- > Open

2. Eliminate water: Edit --> Delete water

3. Find missing atom and repairing them:

Edit → Misc. → Check for missing atoms

Edit → Misc. → Repair missing atoms.

4. Add hydrogens: Edit → Hydrogens → Add → [choose "All hydrogens", "no bond order", and "Yes" to renumbering].

5. Saving receptor file: Grid ➞ Macromolecule ➞ Choose… receptor ➞ Select Molecule . type-in receptor.pdbqt