I wanted to try VFVS on my own set of library and target. I have a file about about 90 compounds which i send through obabel and generated a 3D conformer. I saved the ligand files in pdbqt format and just replace the ligand-library with my own set in the input-folder. I used the same protein as in the prepackaged tutorial. I see that the code is running, but I don’t see any ligand processed when i check using vf_report -c workflow. I am hoping that one of you will be able to help me out. The link to the zip file is here (Zip file)
Did you use the correct hierarchical format for your custom library? As described in the publication and documentation with the four levels of hierarchy (Metatranches, …)? If not, I would recommend to look at the example input ligand library in the tutorial, and structure your library in the same way.
I think I arranged the library in the format of 4 levels. I just had 92 compounds in the library. I have uploaded all the files on google drive. I would appreciate if you could take a look at it and let me if something stands out. Here is the link to the files (LINK)
Did you already try to follow the troubleshooting options which are listed in the documentation?
Also, when you run
vf_report -c workflow, it is not expected to immediately show processed ligands. The ligands are processed in batches (collections), and only when one collection is completed, it will show up as completed by by the
vf_report -c workflow command. Thus it could be that all is just running fine.