Autodock docking analysis: convert dlg to pdb

ligand output poses of the autodock can be converted into the pdb by the following bash code (available at dlg2pdb/dlg2pdb.sh at master · kohlipulkit/dlg2pdb · GitHub):

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read -p "Enter location of dlg file: " location

grep '^DOCKED' $location | cut -c9- > my_docking.pdbqt

cut -c-66 my_docking.pdbqt > dock.pdb

a=$(grep ENDMDL dock.pdb | wc -l)

b=$((a - 2))

csplit -k -s -n 3 -f dock. dock.pdb '/^ENDMDL/+1' '{'$b'}'

read -p "Enter location of macromolecule: " receptor

for f in dock.[0-9][0-9][0-9]

do

mv $f $f.pdb

cat $receptor $f.pdb | grep -v '^END ' | grep -v '^END$' > complex$f.pdb

done

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there are dlg2sdf script availble, as named as mk_copy_coords.py (search you will get it).