a python script to use qvina2 as docking engine to run virtual screening against a database in MDL sdf format.
#prerequisite
- qvina is availale from current PATH
- The full hydrogen is add in the MDL SDF file
- python 3+
- Openbabel 2.4+ for python
- slurm scheduler
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
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