Hi, I ran a Vina docking job (11ac94870d0bb33a811566e8938e5371). The job status showed “okay,” and it apparently ran successfully. However, the output folder is empty; even when I download it to my PC, it is completely empty. Please help
Welcome @victor_igbokwe
It sounds like the VINA Docking job didn’t find any matches with the given Receptor, Ligands, and parameter settings. This could be a valid scientific result .. but we can help to double check that there wasn’t a technical issue with getting the data prepared for this analysis step.
Seeing all of the upstream steps in context will help with troubleshooting. Sharing your history – or workflow invocation – is how to start up a feedback review.
How to share a Workflow Invocation has screenshots in this topic. This is the best way to share work if you used a workflow. → Issues with receiving results from FastQC in MultiQC from several collections of samples - #3 by jennaj.
How to share a history is in this topic. Screenshots are probably not enough for your particular error, especially if there is something we may need to adjust on the server. → How to get faster help with your question
Let’s start there! 
XRef → Hands-on: Protein-ligand docking / Protein-ligand docking / Computational chemistry
Hi @jennaj, thanks a lot for your feedback. I think you have an interesting point that it is possible that the Vina Docking job didnt find matches with the receptor, ligand, and parameter settings.
However, earlier in the day, I ran a similar Vina Docking job (here: 11ac94870d0bb33a1d128f6096b47c1c) using the exact same parameter settings, and it was successful. The difference is that I used just one ligand in that case. I wonder if the error isn’t associated with the number of the ligands contained in the input file.
For clarity, my ligand input file in the subject matter job was a single multi-entry SDF file containing up to 695k ligands. In the parameter, I set the ligand file to be split into its components before the Vina Docking. Do you think the error with the empty output folder could be due to the size and number of the ligand input file?
Meanwhile, I didn’t use a workflow on Galaxy, I simply used the Vina Docking directly. I prepared my receptor properly using MGL Tools Autodock, and I believe the file is properly prepared given that it ran successfully in the first Vina job I ran here on Galaxy.
Here is the link to my history: Galaxy
Please let me know if you need any additional detail.
Thanks so much for your kind assistance.
Hello @victor_igbokwe
Thanks for posting back the history and the screenshots! I can’t see everything due to the sharing on the history, but that’s Ok. With your descriptions, I think I spot the problem.
On the form and down in the Help section, these two statements fit together:
Select ligands (SDF format with multiple ligands or PDBQT format with single ligand).
If using PDBQT format for the ligands only a single ligand can be specified. If using SDF you can include multiple ligands and those ligands are converted to individual PDBQT format files using openbabel as the first step of tool execution.
Then your comments
It looks like the Prepare ligands for docking tool also failed when attempting to split up the SDF file. This is a strong clue about what is going wrong with Vina Docking with that same multi-ligand file (not split). I can’t see the job logs from that tool but you could double check them for some more clues.
Vina Docking error: the message is indicating a problem when attempting to parse out the first ligand. In the details, the job is failing at the step where the tool is applying in the xxy size/center and seed parameters but my guess is the tool was attempting to iterate over those parameters when it read in the upstream longer list of ligands, and that is what triggered the problem.
Argument list too long
Why this didn’t fail is just a corner case – any tool can fail or not and still produce unexpected outputs – it just depends on how much error trapping the original tool author included. Galaxy will inherit anything internal to a scientific tool since our wrappers are around the whole package. My guess is that the tool would fail this way even if run directly, outside of Galaxy. You may be able to find discussion online about this.
What to try
Split inputs
- Prepare your inputs with Prepare ligands for docking OR Prepare ligand
- Input the PDBQT collection to VINA Docking
- Each ligand will have a separate job, and those outputs will be written to a collection.
Or, combined inputs
- Run QA/QC with Prepare ligands for docking OR Prepare ligand (to confirm the format can be read by these tools)
- Input the original multi-ligand to VINA Docking. You may need to test to see how many it can handle at once based on any particular search space parameters you apply (coordinates, but also exhaustiveness and others).
- You could put these parameters into separate file(s) and a simple workflow to run all of this in a batch matrix.
Now, I see some failures already for the prepare ligand steps. I think you’ll need to solve this data content problem first, before running the latter tool, to get around the softer “failure” points. That’s why I am recommending using a splitter as a QC step. Then, if the splitting tool can read the data, Vina Docking tool can also likely also read it.
Hope this helps!
Hi @jennaj,
Thanks a lot for your detailed feedback and suggestions. As you advised, I prepared the ligands by splitting and converting the multi-entry SDF file to PDBQT. The job (11ac94870d0bb33a8c984f34b5a6bb0c) status showed “ok” but with a warning.
Unfortunately, the specific reason for the warning wasn’t stated. Looking at the output note, it shows clearly that it has no dataset in it. This would probably be the third time I have had this same outcome with the prepared ligand. This situation informed my decision to run the Vina Docking with the multi-entry single SDF file.
At this time, I am unable to proceed with the Vina docking job, since the output dataset of the prepared ligand is empty.
Kindly advise me on the next steps to take, please.
Thank you.
If these tools cannot parse or interpret your SDF file, you’ll need to further investigate the content and standardize it.
Search the tool panel with the datatype – you’ll see a few tool options in Galaxy. There is also a viewer, but that won’t you very far since it cannot interpret your file either.
Instead, review the documentation for the underlying tool. There will be guides about the expected formats for the ligand records plus sample data you can compare to. You may also find discussion online about converting formats between the upstream tools you used and downstream tools like this one.
The last option I can think of is to load up the original PDB record and extract the ligand data in Galaxy , instead of uploading these parsed results from some other 3rd party software.
Hope this helps!