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