How to run the VFLP for custerm library

VFLP VFLP 1
#1

Hello all,

When I run the VFLP, the jobs can not be run. The problems are as follows:

** Preparing the to-do lists for jobline 1*
Starting the (re)filling of the todolists of the queues.
Before (re)filling the todolists the queue 1-1-1 had 0 ligands todo distributed in 0 collections.
Before (re)filling the todolists the queue 1-1-2 had 0 ligands todo distributed in 0 collections.

    • Info: No more todo lists.*
    • Warning: There exists an old (locked) todo file. Trying to take care of it…*
    • Warning: The old todo file is a symlink or an empty file. Removing it…*
      The next todo list will be used (todo.all.0000)
    • Info: No more todo lists.*
    • Warning: There exists an old (locked) todo file. Trying to take care of it…*
    • Warning: The old todo file is a symlink or an empty file. Removing it…*
      The next todo list will be used (todo.all.0000)

(1)Do you meet the same bug? Who has the Tutorials for running VFLP?

(2)If I use other ways to generate the pdbqt input files, whether will it impact the final docking results?

(3)For the VSVS, the todo.all file splits the input ligand files into different files. If I just save the input files into one folder, whether will it impact the job distributions?

#2

you can prepare ligand Libs using Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening. After that you have to use open-babel to convert the files in required format for VFVS.

#3

Hey @vas2201, I also prepared my ligands the same way as you mentioned, but I am having issue in using these prepared ligands for docking in vfvs. Did you use your custom prepared ligands to perform docking in VFVS?
Thanks