I am trying to use vfvs_pp_ranking_single.sh in VFtools to prepare the ranking. An error happened for vfvs_pp_firstposes_all_unite.sh 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$ ./vfvs_pp_firstposes_all_unite.sh …/…/…/…/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
CF
I would suggest using vfvs_pp_all.sh 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: vfvs_pp_all.sh <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.
Options:
<smiles_collection_folder>:
* Relative path to the SMILES collection folder
<smiles_collection_folder_format>:
* tranche: smiles_collection_folder/<tranch>/<collection>.smi
* meta_tranche: smiles_collection_folder/<metatranch>/tranch.smi
<database_type>:
* 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"