- May 4, 2022 at 2:59 pm #95104Paul KavanaughGuest
I have been trying to perform some docking with a substrate, but every time I attempt to run the enzyme and substrate, I get a "No such file or directory" error. I have tried to run this in both google chrome and on windows edge, but continue to get this error. The enzyme is in pdbqt format and I drew the substrates in the browser as it is a simple substrate. I am a little confused as to what could be causing this error.
Thank you for the program and your assistance!
- May 4, 2022 at 3:10 pm #95108
It might not be easy to debug, but lets try. After the error is generated, could you please open the browser console (right click anywhere on the page, "inspect", then go to "Console" tab) and run the following command:
And post a screenshot.
- July 28, 2022 at 6:37 am #126825Arthur de FouchierGuest
I’ve been having the same problem.
I’m using a PDB file of a ~430aa protein obbtained from alphafold. For ligand, I’ve been using PBD or SMILES from a 16 carbon chain molecule with an acetate function.
I get the no such file or directory error using Firefox, Chrome and Edge from a Windows 10 Pro computer.
I’ve collected screenshots following your guideline from above. There is 5 of them,. The first one is the result of the command you asked to input. There rest are the messages that appear to me to be webina related.
Here is a link to a Google Photo album with the screenshots. Let me know if you would like me using a different method of sharing screenshots, for futur user with a smiliar problem.
Hope that you can help me using your software.
- August 4, 2022 at 9:46 pm #129504
Sorry for the delay. How do you start the server? Your browser complains of a CORS error.
- August 16, 2022 at 7:50 pm #130720Jaime TamayoGuest
Hi, I’m havinng the same problem. When I try to run any docking it shows: No such file or directory error. I tried to putting the command FS.readdir(‘/’) as you said, but it didn’t work. I would really appreciate that you could check it carefully and fix this problem because I have been using this platform for my thesis work for half a year and it always ran normally. Greetings from Lima, Peru.
- August 16, 2022 at 7:52 pm #130760
Hello. What do you mean it didn’t work? What was the output?
- August 17, 2022 at 2:36 pm #130815Santiago PirelaGuest
I have been using Webina since January. And I have never had any issues with it until Today. I upload my PDB Protein, then my ligand in .mol, and it always shows me an error message saying "Error Converting File. Are you sure it is a properly formatted PDBQT file?" I drew my Ligand on Avogadro and I am having problems running the web server. The ligand is very small actually. I would appreciate any help. Greetings from Colombia.
- August 17, 2022 at 8:08 pm #130928Jacob DurrantKeymaster
Hi Paul and Santiago. Can you send me copies of your protein and ligand files? That would help a lot with debugging. I’ll email you separately. Thanks. ~Jacob
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