qvina2

a python script to use qvina2 as docking engine to run virtual screening against a database in MDL sdf format.

#prerequisite

1. qvina is availale from current PATH
2. The full hydrogen is add in the MDL SDF file
3. python 3+
4. Openbabel 2.4+ for python
5. slurm scheduler

installation

Download:

git clone https://github.com/gkxiao/qvina2.git

Install: put the qvina.py,qvina2_vs_slurm.py and qvina2 in a directory (e.g. ~/bin) which is included in $PATH

usage

step 1. generate slurm batch file

python ~/bin/qvina2_vs_slurm.py -h

usage: qvina2_vs_slurm.py [-h] receptor dbase configure_file output prefix

VS Using QuickVina2

positional arguments:
  receptor        receptor in PDBQT file
  dbase           database in SDF file with full hydrogen
  configure_file  VINA docking configure file
  output          Docking output file in SDF format
  prefix          prefix for SLURM script file

optional arguments:
  -h, --help      show this help message and exit

python ~/bin/qvina2_vs_slurm.py 4no7_prot.pdbqt dbase.sdf config.txt qvina_vs

step 2. submit slurm job

sbatch -N 1 -c 1 qvina_vs.sbatch

CONVERT pdbqt docking pose into sdf file usage:

python pdbqt_pose_2_sdf.py  -h 

example：

python pdbqt_pose_2_sdf.py  PV-000071980170.pdbqt  PV-000071980170.sdf