Hi,

i think it would be better if there would be no log file prior to the running of program hence generating the log file itself. after running of program in command prompt the result may also show in the command prompt revealing the correct operation of vina. the basic application for the opening of log file may also be corrupted.

Hi Joseph Oguegbulu,

keep all your files ie, target.pdbqt, ligand.pdbqt, config.txt and vina.exe in the same directory. Make sure config.txt contains 

receptor = target.pdbqt

ligand = ligand.pdbqt

out = out.pdbqt

center_x = value

center_y = value

center_z = value

size_x = value

size_y = value

size_z = value

use notepad or wordpad to make sure you save as .txt file.

after this your command should work.

All the best... 

Hello everyone, apologies for the late response.

Hi Aditya Rao SJ, like I said earlier, the three files are well saved and in the same folder as vina.exe. And the conf.txt file contains these info as well. That's why I'm surprised it's not running. But thanks for your input. Any other thoughts?

Hi Hira Amjad, if the basic application for opening log file is corrupted, what might be done about it? And secondly, I do not understand what you mean by "it would be better is there was not log file prior to running the application" because there is no log file. 

Hi, DIbakar Pal,

I have followed the thread you provided. Haven't seen similar issues as mine nor any applicable answer.

I'll leave a question though. Thanks

One possibility is there may be a mistake in providing the path in cmd. Can you share the screen shots of your folder..?? Please dont take it in any other sense but have you run vina earlier..?? The same version..?? I am just making sure that the application is not currepted..

No need to apologise Aditya.

No I have not run Vina before. As a matter of fact, I have only just installed the programs. This is my very first time attempting to dock anything. So I can use all the help I can get.

Here's the screenshot of my folder. I do believe that if the path description in CMD was wrong, the error message would be different.

I have also reasoned that perhaps the program might be corrupted, but I wouldn't know. And if it is, then what next, you think?

 Find attached

As far as i have seen both attached files, i assume there is no major issue with vina. i think its all in the basic txt document file. Like the first attachment, the first commend was failed due to some in-appropriation of conf file which is similar to the problem with the log file. please reconsider the notepad you are using for the conf file.

Yes, as Hira Amjad said, the problem is with file format.In your directory you have 3 different type of files ie,.txt, .pdbqt and .exe. But only for .pdbqt files format is visible. I suggest open txt and pdbqt files in text editor and save each with "name.format" in double quotes and then run vina. 

Tried different notepads, still same result.

I'll probably work from another work station, perhaps there's a problem with the vina installation on my pc.

from where you get config config.txt and log log.txt . i want run vina but i do not know from where i can get config config.txt and log log.txt ? how i can generate them?

hi dear

you can write log.txt by notpad++ and save it in the same folder exist your vina then your program will has this error:

could not open "ligand_out.pdbqt" for writing

for solvation that you can write ligand_out.pdbqt by notpad++ and save that

after all your program will work rightly

Hi Azhar salari-jazi

Apparently I had the "could not open ligand_out.pdbqt for writing" error. Is there any fix for this? Been trying everything and nothing seems to be working.

hi ammar shaugi

sorry for late

you can write ligand_out.pdbqt by notpad++ and save it ((name=ligand_out.pdbqt)) in the same folder exist your vina

this error is for your vina path run

another pathway for solvation this problem is cmd running by run as administrator then you can run vina without problem

Thanks Mr. Azhar

I had the same problem and it was solved by writing log.txt and ligand_out.pdbq and saving them in the folder of vina.

Very well Mohammad, good for you.

Many thanks Azhar, I'll try this again when I have something in that regard to work on.

This issue is seen when you dont have administrative right in your working folder. You may try doing the same in a system/folder with administrative rights.

hi dear

i have the same error and i do many ways to solve that but all of these ways could not help me.

at last i find what is the problem.

you should copy vina folder and paste it in other place such as drive D or .... and run vina in this new location.

the problem was in place of vina folder in this address "C:\Program Files (x86)\The Scripps Research Institute\Vina"

because the computer dose not let vina to create file in this location

best

For all the researchers working on Linux. Vina works just fine and does not show this error.

For the researchers working on Windows, do not keep the "The Scripps Research Institute" folder in the C:/ drive. Vina.exe does not work from C:/ directory. Copy the whole folder to any other alternative directory and run the Commandline in that copied directory. It won't show this error.

Hi Dear friends,

Here, there is a good topic and of course a good discussion,

In my idea, the main reason for some repeating errors in Vina is due to this: "Destination folder access denied".

You can use this software "TakeOwnerSship Pro".

It gives users the opportunity to take full file and folder ownership permission, and in this case, provide full access to Vina.exe to be run completely. This app is very easing to use. I think it solves the error "ligand_out.pdbqt".

Best