VFVS Analysis using VF tools : Not creating firstposes.all.minindex.sorted.clean file

Dear All,

I am doing analysis of the docking results and trying to find the ranking/qvina02_rigid_receptor1 folder to use the head command that mentioned in the tutorial. But I didn’t find the folder path (ranking/qvina02_rigid_receptor1 ) in the out-put files. So could you please clarify or guide me that what i am missing here ?

head -n 100 …/…/ranking/qvina02_rigid_receptor1/firstposes.all.minindex.sorted.clean > compounds.


while using the first command , i am getting the following error.

[srp106@hpc4 ranking]$ vfvs_pp_ranking_all.sh …/…/output-files/complete/ 2 meta_tranch

  • Starting to prepare the firstposes of docking-scenario qvina02_rigid_receptor1
    [1]+ Running vfvs_pp_ranking_single.sh $input_folder/$folder ${library_format} &

  • Starting to prepare the firstposes of docking-scenario smina_rigid_receptor1

  • The folder qvina02_rigid_receptor1 exists already, exiting.

  • The folder smina_rigid_receptor1 exists already, exiting.
    awk: fatal: cannot open file qvina02_rigid_receptor1/firstposes.all.minindex.sorted.clean' for reading (No such file or directory) awk: fatal: cannot open file smina_rigid_receptor1/firstposes.all.minindex.sorted.clean’ for reading (No such file or directory)

  • The first-poses of all docking runs have been prepared

[srp106@hpc4 ranking]$ bash: line 0: kill: (-22948) - No such process

[srp106@hpc4 ranking]$

Thank you

Looks like when I used the first command, It is not preparing the firstposes.all.minindex.sorted.clean, I can only see firstposes.all.minindex file. it is empty.

FYI : I kept the the VFTools/bin in my PATH and also obabel command is available in my root.

Okay ! Here I found something …After fixing it, there are no more errors while doing ligand ranking and extracting docking poses.

If you specified the mode of outputfiles_level as collection in all.ctrl file. (outputfiles_level=collection )
After creating pp/ranking folder, change to the directory in to ranking folder as per the tutorial. Use the the below command while doing ligand ranking,
vfvs_pp_ranking_all.sh …/…/output-files/complete/ 2 meta_collection

If you specified the mode of outputfiles_level as tranch in all.ctrl file. outputfiles_level=tranch
use the the below command while doing lignad ranking
vfvs_pp_ranking_all.sh …/…/output-files/complete/ 2 meta_tranche

FYI : all.ctrl file options :

Possible values:

* collection : The collection output files are stored in tar.gz format. They are stored in subfolders named by metatranch and tranch to reduce the number of files per folder.


* Less I/O on the shared cluster file system (as existing tranch archives don’t have to be read during storage of completed collectionsds)

* No risk of output-file clashes when two queues want to store completed collections on the shared filesystem

* tranch : For each tranch a tar archive is created, which contains the gzipped collection output files.


* Less output files (only for each tranch) for each of the output file types (e.g. results, summaries, logfiles, …)

I recently ran into the same problem.

The reason as you pointed it out was that the qvina02_rigid_receptor1/firstposes.all.minindex.sorted.clean file was not created because I was not using the right argument in :

vfvs_pp_ranking_all.sh …/…/output-files/complete/ 2 <INSERT_ARGUMENT_HERE>

Depending the code version I think it should be meta_tranch or meta_tranche

However, if you already ran vfvs_pp_ranking_all.sh once it won’t look at creating the file when you run it again and directly look for that sorted.clean file, won’t find it and skip. In my case, deleting the ranking data from pp/ranking/ and re-running with the right argument fixed the issue, created the qvina02_rigid_receptor1/firstposes.all.minindex.sorted.clean file and the rest of the ranking proceeded without issues.

Im gonna try this fix for my own problem, for me it seems to only prepare the first docking pose as well out of all. Not sure if its because of what you guys mention but well

Hi Kaneki,
are you able to fix the problem with docking poses ?.