I think you have not saved the file as needed. when you save the protein file after grid box formation in the output step write its full name as "protein.pdbqt" it will be saved, then try to open this file you will find it.

Thanks for the comment. Finally I made the program work. The recipe to do this? 1. Install the program without changing any path. 2. Create a new folder where you like and put inside the ligand and the enzyme, etc.. 3. When running AutoDockTools provide only the path for the *.exe files and your input (pdb) files. 4. When keeping any file, let the progran choose and modify nothing. 5. Up to this point all works nice and the corresponding files are generated (see inside what folder in your case).

Dear Gómez-Jeria

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

Thank you very much. Regards, Juan.

Dear Juan

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

[email protected]

I'm at your service for any help.

Excuse me.

I have a problem with vina, I try to do:

./vina --config ***.txt --receptor ***.pdbqt --out ***.pdbqt --log log_***.txt

But, I have a problem with the receptor...

"Parse error on line 2 in file "receptor.pdbqt": Unknown or inappropriate tag."

I saw the 2 line of the document but it is normal.

ATOM 1 N MET 1 1.313 -31.540 -81.493 1.00 0.00 -0.058 N

ATOM 2 HN1 MET 1 1.731 -30.924 -80.796 1.00 0.00 0.276 HD ...

I can`t find information about this.

Could you help me with this?

Ani Pulido same problem is happening here. you got solution?

If you get it let me know

Thank you

i am facing the same problem i can run autogrid but not autodock after giving run its giving "cant find or pdbqt file for ligand.

i also saved the ligand in pdbqt format

can any let me know what will be the solution

@Saranya Shivashankar Autodock has a problem with spaces in the directory path. If it can't find or open receptor then it's probably because of a space in the name of your working directory(folder). I suggest you use one name or separate 2 names with underscore

My suggestion is to use Autodock on Ubuntu, it is more compatible and give no or fewer errors.

Hello Folks,

I am also trying to do some docking experiments but everytime I open the ligand file the Autodock closes automatically. I do not know where the exact problem is. The possible solutions will be highly appreciated.

Dear Deppti,

It seems an installation problem, two questions:

1) Are you running Autodock in linux or windows?

2) What version of ADT do you have?

Hello Martiniano

I am using Autodock 4.2.5 installed on windows 10. I sorted out this problem by saving the ligand file in mol and converts it to pdbqt. Its working fine now but the new problem arises. It is showing some error of uncompleted task as autogrid is unable to read the grid file.

Hi, Deepti

Try to check if the grid parameters you selected are present in gpf file.

Hello Bello

Ok I will surely try this.

Dear Deepti

Did you find any solutions for this. I am also facing the same trouble.

The error log says Sorry, I can't find or open Grid Parameter File "C:/Users/jagannath/Desktop/Docking". I had saved all the files in a Folder in desktop and set the folder in the prefernces. The gpf file is present in the specified folder. But still it is not able to read or find the gpf file. Could you please Collins Kigen Ashraf Ahmed Abdusalam Ashraf Ahmed AbdusalamMartiniano Bello

@Arabinda I am wondering whether have you copied the Autogrid4 and autodock4 file into the working desktop folder..

Also I noticed that cmd working location is not in Desktop folder

Yes Shafi you are right as so many persons has figured out this as a potential solution.

While working with autodock tools 1.5.6, the auto Grid has running normally until the end of calculation but the Auto Dock figure this kind of error :

WARNING: Unrecognized PDBQT record type in line ,

ERROR: All ATOM and HETATM records must be given before any nested BRANCHes; see line 79 in PDBQT file "A.pdbqt".

Whould you please help me if you know the error and how to solve it, thank you

Perhaps there must be some problem with naming your files.

Also try using scripts that will help you reduce manual errors.

Pls visit this link: http://autodock.scripps.edu/faqs-help/how-to/how-to-setup-adt-scripts

Hi Arabinda Mahanty , I experienced exactly the same thing (see attached screenshot). I am using Autodocktools-1.5.6 on windows 10. can anyone please provide some hints???

Hi, Wayan Mudianta

check whether autogrid4.exe and autodock4.exe files are placed in the same folder which you are working on and also make sure that files has been named properly.

Hello Bli Wayan Mudianta ,

The problem is on the name of your workspace folder, it contains space character. Just rename your workspace folder, and try to docking again. I hope it will solve your problem.

Hi,

I have faced similar problem. As Mr. Dian said, the workspace folder name or the directory to the folder should not contain any space. That is the folder where you have your autogrid and autodock extension files and other files such as pdb, pdbqt, gpf, dpf etc should be named without space. If you could not rename that folder just create a new folder directly in your C:. Copy the path name and paste in the file>prefernces>set>startup directory and make it as default. These steps helped to overcome the issue. Hope it will solve your problem too.

Hi,

I have some problems same as people above. I am pretty sure that there is no space character, but why I can not run AutoGrid? Can anyone help me?

Nur Fitria

If not spacing error check whether all the files (target and receptor) along with autogrid4 and autodock4 extension are placed in same working folder.

Hi, I checked, I have no spaces in any of the files or the workspace, I have all four files of autodock4, autogrid4, AD4.1_bound and AD4 parameters in the same folder along with others. I am still facing the error .. kindly help

Setting the Working directory solved problem for me..

open ADT> File> Preferences>set> Startup Directory(copy and paste the working directory path) for example: “C:\Users\project or any other directory where you have all files as said earlier.

Save all the PDB,PDBQT,GLG,autogrid.exe and autodock.exe in same folder and use It as single directory. Then run autogrid to by selecting autogrid.exe and grid.gpf

Hope this should solve..It solved for me..

@Hema Rubesh I have done all these steps.. it still does not work. Is there any other possible issue?

Moksha Mehta I Opened your dlg file and came to know that the working directory is correct. Now try checking the file extension of your pdbqt files in your folder.If not in pdbqt format save it so..

Hema Rubesh Hi, I checked that as well. I do have the files in pdbqt format all in the same folder. Could there be any other issue?

Nur Fitria Hi, I am also facing the same problem. Could you find a solution?

Hi, I am facing a problem with Autodock. while analyzing, I cannot upload the macromolecule as it shows the macromolecule is not found in this directory and I am receiving the following error.

55, in post_traverse

apply(c.post_traverse, a, kw)

File "C:\Users\Sumedha\autodock\lib\site-packages\mglutil\util\tree.py", line 55, in post_traverse

apply(c.post_traverse, a, kw)

File "C:\Users\Sumedha\autodock\lib\site-packages\mglutil\util\tree.py", line 55, in post_traverse

apply(c.post_traverse, a, kw)

File "C:\Users\Sumedha\autodock\lib\site-packages\mglutil\util\tree.py", line 55, in post_traverse

apply(c.post_traverse, a, kw)

File "C:\Users\Sumedha\autodock\lib\site-packages\mglutil\util\tree.py", line 55, in post_traverse

apply(c.post_traverse, a, kw)

File "C:\Users\Sumedha\autodock\lib\site-packages\mglutil\util\tree.py", line 55, in post_traverse

apply(c.post_traverse, a, kw)

File "C:\Users\Sumedha\autodock\lib\site-packages\mglutil\util\tree.py", line 55, in post_traverse

apply(c.post_traverse, a, kw)

File "C:\Users\Sumedha\autodock\lib\site-packages\mglutil\util\tree.py", line 55, in post_traverse

apply(c.post_traverse, a, kw)

File "C:\Users\Sumedha\autodock\lib\site-packages\mglutil\util\tree.py", line 55, in post_traverse

apply(c.post_traverse, a, kw)

RuntimeError: maximum recursion depth exceeded

ERROR *********************************************

Traceback (most recent call last):

File "C:\Users\Sumedha\autodock\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto

result = command( *args, **kw )

File "C:\Users\Sumedha\autodock\lib\site-packages\AutoDockTools\autoanalyzeCommands.py", line 1393, in doit

macro.buildBondsByDistance()

AttributeError: 'str' object has no attribute 'buildBondsByDistance'

Can anyone please help?

Hii

I am facing this error while running autogrid.

Could anyone pls let me know how to rectify it

Python 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 bit (Intel)] on win32

Type "copyright", "credits" or "license()" for more information.

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

Personal firewall software may warn about the connection IDLE

makes to its subprocess using this computer's internal loopback

interface. This connection is not visible on any external

interface and no data is sent to or received from the Internet.

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

IDLE 1.2.2 ==== No Subprocess ====

>>> ERROR *********************************************

Traceback (most recent call last):

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto

result = command( *args, **kw )

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 968, in doit

self.vf.ADstart_manage.addProcess(ps)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 269, in addProcess

if not self.kill.master.winfo_ismapped() and not self.kill.done:

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\lib-tk\Tkinter.py", line 749, in winfo_ismapped

self.tk.call('winfo', 'ismapped', self._w))

TclError: bad window path name ".404123200"

ERROR *********************************************

Traceback (most recent call last):

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto

result = command( *args, **kw )

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 968, in doit

self.vf.ADstart_manage.addProcess(ps)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 269, in addProcess

if not self.kill.master.winfo_ismapped() and not self.kill.done:

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\lib-tk\Tkinter.py", line 749, in winfo_ismapped

self.tk.call('winfo', 'ismapped', self._w))

TclError: bad window path name ".404123200"

ERROR *********************************************

Traceback (most recent call last):

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto

result = command( *args, **kw )

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 968, in doit

self.vf.ADstart_manage.addProcess(ps)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 269, in addProcess

if not self.kill.master.winfo_ismapped() and not self.kill.done:

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\lib-tk\Tkinter.py", line 749, in winfo_ismapped

self.tk.call('winfo', 'ismapped', self._w))

TclError: bad window path name ".404123200"

ERROR *********************************************

Traceback (most recent call last):

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto

result = command( *args, **kw )

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 968, in doit

self.vf.ADstart_manage.addProcess(ps)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 269, in addProcess

if not self.kill.master.winfo_ismapped() and not self.kill.done:

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\lib-tk\Tkinter.py", line 749, in winfo_ismapped

self.tk.call('winfo', 'ismapped', self._w))

TclError: bad window path name ".404123200"

ERROR *********************************************

Traceback (most recent call last):

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto

result = command( *args, **kw )

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 968, in doit

self.vf.ADstart_manage.addProcess(ps)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 269, in addProcess

if not self.kill.master.winfo_ismapped() and not self.kill.done:

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\lib-tk\Tkinter.py", line 749, in winfo_ismapped

self.tk.call('winfo', 'ismapped', self._w))

TclError: bad window path name ".404123200"

charges on carbons unchanged

ERROR *********************************************

Traceback (most recent call last):

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto

result = command( *args, **kw )

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 968, in doit

self.vf.ADstart_manage.addProcess(ps)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 269, in addProcess

if not self.kill.master.winfo_ismapped() and not self.kill.done:

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\lib-tk\Tkinter.py", line 749, in winfo_ismapped

self.tk.call('winfo', 'ismapped', self._w))

TclError: bad window path name ".404123200"

5meo:A:HIS3 missing both hydrogens!

5meo:A:HIS70 missing both hydrogens!

5meo:A:HIS74 missing both hydrogens!

5meo:A:HIS93 missing both hydrogens!

5meo:A:HIS114 missing both hydrogens!

5meo:A:HIS145 missing both hydrogens!

5meo:A:HIS151 missing both hydrogens!

5meo:A:HIS188 missing both hydrogens!

5meo:A:HIS191 missing both hydrogens!

5meo:A:HIS192 missing both hydrogens!

5meo:A:HIS197 missing both hydrogens!

5meo:A:HIS260 missing both hydrogens!

5meo:A:HIS263 missing both hydrogens!

polar hydrogens missing from n-terminus of chain A

charges on carbons unchanged

ERROR *********************************************

Traceback (most recent call last):

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto

result = command( *args, **kw )

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 968, in doit

self.vf.ADstart_manage.addProcess(ps)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 269, in addProcess

if not self.kill.master.winfo_ismapped() and not self.kill.done:

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\lib-tk\Tkinter.py", line 749, in winfo_ismapped

self.tk.call('winfo', 'ismapped', self._w))

TclError: bad window path name ".404123200"

ERROR *********************************************

Traceback (most recent call last):

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto

result = command( *args, **kw )

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 968, in doit

self.vf.ADstart_manage.addProcess(ps)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 269, in addProcess

if not self.kill.master.winfo_ismapped() and not self.kill.done:

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\lib-tk\Tkinter.py", line 749, in winfo_ismapped

self.tk.call('winfo', 'ismapped', self._w))

TclError: bad window path name ".404123200"

ERROR *********************************************

Traceback (most recent call last):

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto

result = command( *args, **kw )

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 968, in doit

self.vf.ADstart_manage.addProcess(ps)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 269, in addProcess

if not self.kill.master.winfo_ismapped() and not self.kill.done:

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\lib-tk\Tkinter.py", line 749, in winfo_ismapped

self.tk.call('winfo', 'ismapped', self._w))

TclError: bad window path name ".404123200"

5meo:A:HIS3 missing both hydrogens!

5meo:A:HIS70 missing both hydrogens!

5meo:A:HIS74 missing both hydrogens!

5meo:A:HIS93 missing both hydrogens!

5meo:A:HIS114 missing both hydrogens!

5meo:A:HIS145 missing both hydrogens!

5meo:A:HIS151 missing both hydrogens!

5meo:A:HIS188 missing both hydrogens!

5meo:A:HIS191 missing both hydrogens!

5meo:A:HIS192 missing both hydrogens!

5meo:A:HIS197 missing both hydrogens!

5meo:A:HIS260 missing both hydrogens!

5meo:A:HIS263 missing both hydrogens!

polar hydrogens missing from n-terminus of chain A

ERROR *********************************************

Traceback (most recent call last):

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto

result = command( *args, **kw )

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 968, in doit

self.vf.ADstart_manage.addProcess(ps)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 269, in addProcess

if not self.kill.master.winfo_ismapped() and not self.kill.done:

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\lib-tk\Tkinter.py", line 749, in winfo_ismapped

self.tk.call('winfo', 'ismapped', self._w))

TclError: bad window path name ".404123200"

ERROR *********************************************

Traceback (most recent call last):

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto

result = command( *args, **kw )

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 968, in doit

self.vf.ADstart_manage.addProcess(ps)

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autostartCommands.py", line 269, in addProcess

if not self.kill.master.winfo_ismapped() and not self.kill.done:

File "C:\Program Files (x86)\MGLTools-1.5.6\lib\lib-tk\Tkinter.py", line 749, in winfo_ismapped

self.tk.call('winfo', 'ismapped', self._w))

TclError: bad window path name ".404123200"

Priya Singh

A friend of mine encountered the same error while using autodock4.2.

Probable reasons for your error

1) Your ligand is high molecular weight protein. You can try softwares specifically for protein-protein docking.

This answer will be helpful for protein-protein docking.

https://www.researchgate.net/post/Protein-Protein_Docking

2) Installation error

A few pointers to note:

a) It is recommended to install the applications (autodock 4.2, MGL tools and python) in default directory.

b) It is also recommended to install python. The version we installed is python 3.8 on a AMD 64 bit processor. You can install the 32 or 64 bit version depending upon your system configuration.

c) Ensure that autodock4.exe, autogrid4.exe, AD4_parameter and AD4_bound files are copied to your workspace folder.

d) Ensure that you set the working folder directory before starting your work on autodock4.2.

e) Ensure that your receptor and ligand preparation is done correctly.

I hope these tips help.

Good luck !

Please how can I solve the issue of ''/cygdrive/c/ADTWORKSPACE/autodock4: I'm sorry; I can't find or open "6LU7.Ag.map" in autodock. I keep on getting this on my .dlg file . i have been trying to dock a silver complex molecule to a protein after series of editing the parameter files. Please help me, I have atttached the screenshot of the dlg file