LigFlow

Description

LigFlow is a tool designed to select and parametrize your docking poses before using ScoreFlow.

When to use LigFlow

➡️ If you want to run ScoreFlow on a subset of docking poses : the "BEST" mode.
➡️ If you want to run MM(PB,GB)SA calculations with ScoreFlow.

Usage

LigFlow

• -h|--help : Show this help message and quit
• -f|--file : Read the docking poses to prepare directly from this file. Organization of the file :
  • CSV format
  • 1 line per docking pose
  • field 1 : name of the folder containing the pose in the "docking" directory
  • field 2 : name of the ligand
  • field 3 : name of the docking pose (no ".mol2" extension)
    Example of a line :

    decoys_1_100,ZINC02617749,ZINC02617749_conf01

• -c|--cutoff FLOAT : Only the poses with a score below or equal to this cutoff will be extracted.
  • Default : 0
• -np|--nbposes INT : Restrict preparation to the X best poses per ligand.
  • Default : None. Keep all poses.
• -d|--docking PATH : Path to the docking folder.
  • Default : $PWD/docking
• -at|--atomtype TYPE :
  • gaff : used for MM(PB,GB)SA
  • gaff2
  • amber
  • bcc
  • sybyl
  • Default : gaff if different charges are specified, else None (keep current)
• -ch|--charge TYPE :
  • gas : Gasteiger
  • bcc : AM1-BCC
  • resp : RESP
  • Default : None. Keep existing charges
• -p|--purge : Delete all previous ligands configuration
• -a|--amber : Prepare frcmod and lib files for MM(PB,GB)SA
• -rst|--restart : Restart from errors.csv
• -r|--run MODE :
  • local
  • parallel : not recommended for RESP charges
  • mazinger
  • Default : local
• -cn|--corenumber INT : Number of cores for parallel, mazinger, and/or RESP charges.
  • Default : 8
• -mem|--memory INT : Memory allocated for computing RESP charges.
  • Default : 8GB
• -max|--maxsub INT : Maximum number of jobs to submit to mazinger.
  • Default : None. 1 job per pose

Results

The prepared docking poses will be located inside the input_files/lig directory.

In case of errors, an error.csv file will be available inside the run folder.

Example

1. Preparation of a subset of your docking poses based on their score and a restriction on the number of poses per ligand, to run MM-PB-SA with ScoreFlow :

LigFlow --cutoff -104.4 -np 3 -at gaff --amber --run parallel

❓ I did a virtual screening without DockFlow. Can I still use LigFlow ?

Yes, but you will need to adapt the structure of your files to the one DockFlow uses :

1. First, follow the guideline in ScoreFlow's FAQ.
2. Create a ranking_sorted.csv file in the directory of the first step. The format of this file is as follows :
   name_of_docking_pose,score. Other fields can be present in the file, they will not be used by LigFlow. This file must be sorted by score (most negative score at the top of the file).
   Example of a line :

   ZINC02617749_conf01,-110.3

3. Create a directory containing your original ligands used for docking, in MOL2 format (1 or more compounds per MOL2 file).
4. Create a DockFlow.config inside the directory of the first step with the following line : lig_folder="path/to/directory/from/step3"