A question on VFLP input format

Can someone please provide some more details on how to prepare the input data for VFLP? Below are the steps I followed to run the pipeline.

  1. I’ve got a bunch of smile files that I curated by hand. I kept them in the following structure:
|___ ligand1.smi
|___ ligand2.smi
  1. After running ./vf_prepare_folders.sh, I start the jobs with the following command
./vf_start_jobline.sh 1 2 templates/template1.slurm.sh submit 1
  1. The job does start with the following output
Syncing the jobfile of jobline 1 with the controlfile file ../../workflow/control/all.ctrl.
Syncing the jobfile of jobline 2 with the controlfile file ../../workflow/control/all.ctrl.

Submitted batch job 2
The job for jobline 1 has been submitted at Mon Sep  7 09:57:12 UTC 2020.

Submitted batch job 3
The job for jobline 2 has been submitted at Mon Sep  7 09:57:13 UTC 2020.
  1. But once the jobs are finished, I don’t see any output in the output-files folder. Is it because of the wrong input file structure?
  2. Can I just add smiles files as input-files/*.smi or do I need input-files/ligand-library/*.smi ?
  3. Or do I need a deeper level hierarchy like tranche names? If yes, then how do I decide, which letters to use for defining the meta-tranche?
  4. Do I also need to make any changes in todo.all or anywhere else? If yes, what changes?


1 Like

Hi I would like some more info on the input format as well. I have one massive .smi file with all the compounds and don’t know if VFLP will split them into separate pdbqt’s for me.

Hi @janujan9954 and @mnis ,

Welcome to the forum @mnis :slight_smile:

The question was already posted a few times, see for instance here:

Hope this helps,