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

put the qvina.py,qvina2_vs_slurm.py and qvina2 in ~/bin which is availabe 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

step 2. submit slurm job

sbatch -N 1 -c 1