export PATH=${PATH}:/home/preps/golovin/progs/bin
export MOPAC_LICENSE=/home/preps/golovin/progs/bin
for i in nag_h nag_oh nag_nh2 nag_ph ;do
obgen ${i}.smi > ${i}.mol
babel -imol ${i}.mol -opdb ${i}.pdb 
babel -ipdb ${i}.pdb -omop ${i}.mop -xk "PM6" 
MOPAC2009.exe ${i}.mop 
babel -imopout ${i}.out -opdb ${i}1.pdb
/home/preps/golovin/progs/bin/prepare_ligand4.py -l ${i}1.pdb -o ${i}.pdbqt
vina --config vina.cfg --receptor seq5.pdbqt --ligand ${i}.pdbqt --out ${i}_seq5.pdbqt --log ${i}_seq5.log
vina --config vina.cfg --receptor seq5_rigid.pdbqt --flex seq5_flex.pdbqt --ligand ${i}.pdbqt --out ${i}_seq5_flex.pdbqt --log ${i}_seq5_flex.log
done







