Complete ligand ranking using

Dear community,

I am trying to use in VFtools to prepare the ranking. An error happened for as below. it complains the folder does not exist but it exist as you can see from the result of ls command. Is there anything I did wrong? Thanks.

(base) tm@tm:~/tangm5/carp/vftutorial/VFVS_GK/pp/ranking/VFTools/bin/smina_rigid_receptor1$ ./ …/…/…/…/output-files/complete/smina_rigid_receptor1/summaries tar firstposes.all

         Creating a single file with all first poses             

ls: cannot access ‘…/…/…/…/…/output-files/complete/smina_rigid_receptor1/summaries’: No such file or directory

  • Cleaning the temporary files *

  • All first poses have been united in the file firstposes.all
    (base) tm@tm:~/tangm5/carp/vftutorial/VFVS_GK/pp/ranking/VFTools/bin/smina_rigid_receptor1$ ls …/…/…/…/…/output-files/complete/smina_rigid_receptor1/summaries

Hi Tammy and welcome to the forum,

I would suggest using if you want to extract the poses and/or prepare a list of the top scoring compounds.

Here is a short explanation on what argument you can use (this pops up if you simply run the script without any argument as well):

usage="Usage: <smiles_collection_folder> <smiles_collection_folder_format> <database_type> <dwar_compound_count> <poses_compound_count>
This script has to be run in the root folder of the VirtualFlow installtion directory.
This script post-processes the virtual screening data, and stores the post-processsed files in the folder pp (postprocessing). More specifically, it does the following:
    1) It prepares the full ranking of all docking compounds for each docking scenario, and stores it in the folder pp/firstposes.
    2) It exctracts and reformats the docking poses of the best <poses_compound_count> compounds, and stores it in the folder pp/docking_poses.
    3) It prepares the input files for DataWarrior for the best <dwar_compound_count> compounds, and stores it in the folder pp/dwar.
The preparation of the docking poses when the receptor was allowed to be flexible might not work perfectly yet.
      * Relative path to the SMILES collection folder
      * tranche: smiles_collection_folder/<tranch>/<collection>.smi
      * meta_tranche: smiles_collection_folder/<metatranch>/tranch.smi
      * ZINC15: Prepares also the vendor availability according to the ZINC library
      * Other: No preparation of vendor availability
    <dwar_compound_count>: Number of dwar compounds
    <poses_compound_count>: Number of compounds for which the docking poses should be prepared"