I have all the files ligand + receptor (both in pdbqt)+ all vina files vina.exe ,vina_license+vina split +conf txt in a single folder.
I keep getting this error when I try to run docking in command prompt. here I attached the picture of the error and my txt.
I am very new to this field, appreciate your help.
Hello Mina Poursharifi,
I was also facing the same error. The error can be a consequence of using flexible ligand PDBQT which is not acceptable in vina. AutoDockTools can be used to handle that. If you are using openbabel for file format conversion for ligand libraries, then try using the 'r' option.
You can also refer this thread. http://mgldev.scripps.edu/pipermail/autodock/2017-June/010596.html
Thank you
Mina Poursharifi
" I have all the files ligand + receptor (both in pdbqt)+ all vina files "
i believeI this is your mistake, you have to separate the receptor and ligand before docking them.
best regards
Share the screenshot of the folder where the files are stored? it looks like some file missing in the folder.
Hello Ms. Mina,
It could be that the name of the ligand is somewhat different frome the name you typed in the conf.txt file, like having capital letters in the pdbqt structure filename but not typing them in the conf.txt file. Let me know if this was helpful.
Best regards
Hi Mina,
I agree with Randy. The problem is due to the fact that the file name of the ligand does not match the one you indicate in the conf file.
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