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Well, I imagine you could pass it to openbabel to try and convert it. Something like:
obabel large_file.sdf -Onew.smi -m
Then check whether the number of the output files is equal to the number of compounds in the input file.Hello.
Webina mimics Autodock Vina’s behavior by producing the only output file which contains the original receptor and ligand docked. You can access the file on the output tab after a successful run. I just checked that we don’t have a bug there. It’s not the ligand file that you can download. It should be the complex.
I hope this helps.
Best regards,
Yuri
P.S. I want to highlight, that "mimic" might not be the right term. Webina is actually AutoDock Vina compiled for Web assembly. Webina simply outputs whatever Vina produces. It doesn’t alter the resulting file in any way.It was me who has actually updated blenmol for 2.8 Haven’t tested it for 2.9 yet. Will look at the issue soon. Does it happen for any proteins or could you please provide some specific pdb(s)?
Best regards,
YuriI wouldn’t suggest doing this, to begin with. Yet if no other solution is available, I would assume it makes sense to change the perms before the files are accessed. For example, in:
/home/witte.t/autogrow4/autogrow/plotting/generate_line_plot.py
You could add
import os
after line 8
Then, after line 86 (after the loopfor rank_file in ranked_file:)
os.chmod(rank_file , 0777)
Disclaimer: I’m not the author of autogrow project. This all looks like a poor man’s solution. Ideally would be to deal with the OS setup, so that the files would be accessible with no tweaks.
Let’s try and call someone else to help you.Still looks like a permission error to me. It’s either the ranked file(s) that was not created or it’s empty. Would you mind checking?
ls -lR | grep "_ranked.smi"hello. What are the permissions of the receptor.pdb? I.e.
ls -l /home/witte.t/autogrow4/tutorial/PARP/4r6eA_PARP1_prepared.pdb
