
Convert ligand file format also add H
babel -isdf ligand.sdf -opdbqt ligand.pdbqt -h

#add H to protein
#babel -ipdbqt 830cA.pdbqt -opdbqt 830cA-H.pdbqt -h

Get the ligand center as location of virtual screening:
babel -ipdbqt ligand.pdbqt -obox > ligand.center


Get virtual screening box size:
perl ~/scripts/box-gyration.pl ligand.sdf

convret result to .pdb format
babel -ipdbqt vina_best.pdbqt -opdb vina_best.pdb

run vina
vina --config config.txt
