Converting SDF to PDBQT using OpenBabel

Question

I want to convert several molecules from sdf format to pdbqt using OpenBabel.

However, I can't find pdbqt format neither in the output format options nor in the input.

I tried reinstalling MGLTools, as it has AutoDock, but the issue remains.

Answer 1

Please, check the version of OpenBabel you are using. At least, version 3.1.0 has the pdbqt format implemented:

# obabel -v
No input file or format spec or possibly a misplaced option.
Most options must come after the input files. (-i -o -O -m can be anywhwere.)

Open Babel 3.1.0 -- Jan 11 2021 -- 11:51:22

and:

# obabel -L formats
abinit -- ABINIT Output Format [Read-only]
acesin -- ACES input format [Write-only]
acesout -- ACES output format [Read-only]
acr -- ACR format [Read-only]
adf -- ADF cartesian input format [Write-only]
adfband -- ADF Band output format [Read-only]
adfdftb -- ADF DFTB output format [Read-only]
adfout -- ADF output format [Read-only]
alc -- Alchemy format
aoforce -- Turbomole AOFORCE output format [Read-only]
arc -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
ascii -- ASCII format [Write-only]
axsf -- XCrySDen Structure Format [Read-only]
bgf -- MSI BGF format
box -- Dock 3.5 Box format
bs -- Ball and Stick format
c09out -- Crystal 09 output format [Read-only]
c3d1 -- Chem3D Cartesian 1 format
c3d2 -- Chem3D Cartesian 2 format
cac -- CAChe MolStruct format [Write-only]
caccrt -- Cacao Cartesian format
cache -- CAChe MolStruct format [Write-only]
cacint -- Cacao Internal format [Write-only]
can -- Canonical SMILES format
car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
castep -- CASTEP format [Read-only]
ccc -- CCC format [Read-only]
cdjson -- ChemDoodle JSON
cdx -- ChemDraw binary format [Read-only]
cdxml -- ChemDraw CDXML format
cht -- Chemtool format [Write-only]
cif -- Crystallographic Information File
ck -- ChemKin format
cml -- Chemical Markup Language
cmlr -- CML Reaction format
cof -- Culgi object file format
com -- Gaussian Input [Write-only]
confabreport -- Confab report format [Write-only]
CONFIG -- DL-POLY CONFIG
CONTCAR -- VASP format
CONTFF -- MDFF format
copy -- Copy raw text [Write-only]
crk2d -- Chemical Resource Kit diagram(2D)
crk3d -- Chemical Resource Kit 3D format
csr -- Accelrys/MSI Quanta CSR format [Write-only]
cssr -- CSD CSSR format [Write-only]
ct -- ChemDraw Connection Table format
cub -- Gaussian cube format
cube -- Gaussian cube format
dallog -- DALTON output format [Read-only]
dalmol -- DALTON input format
dat -- Generic Output file format [Read-only]
dmol -- DMol3 coordinates format
dx -- OpenDX cube format for APBS
ent -- Protein Data Bank format
exyz -- Extended XYZ cartesian coordinates format
fa -- FASTA format
fasta -- FASTA format
fch -- Gaussian formatted checkpoint file format [Read-only]
fchk -- Gaussian formatted checkpoint file format [Read-only]
fck -- Gaussian formatted checkpoint file format [Read-only]
feat -- Feature format
fh -- Fenske-Hall Z-Matrix format [Write-only]
fhiaims -- FHIaims XYZ format
fix -- SMILES FIX format [Write-only]
fps -- FPS text fingerprint format (Dalke) [Write-only]
fpt -- Fingerprint format [Write-only]
fract -- Free Form Fractional format
fs -- Fastsearch format
fsa -- FASTA format
g03 -- Gaussian Output [Read-only]
g09 -- Gaussian Output [Read-only]
g16 -- Gaussian Output [Read-only]
g92 -- Gaussian Output [Read-only]
g94 -- Gaussian Output [Read-only]
g98 -- Gaussian Output [Read-only]
gal -- Gaussian Output [Read-only]
gam -- GAMESS Output [Read-only]
gamess -- GAMESS Output [Read-only]
gamin -- GAMESS Input
gamout -- GAMESS Output [Read-only]
gau -- Gaussian Input [Write-only]
gjc -- Gaussian Input [Write-only]
gjf -- Gaussian Input [Write-only]
got -- GULP format [Read-only]
gpr -- Ghemical format
gr96 -- GROMOS96 format [Write-only]
gro -- GRO format
gukin -- GAMESS-UK Input
gukout -- GAMESS-UK Output
gzmat -- Gaussian Z-Matrix Input
hin -- HyperChem HIN format
HISTORY -- DL-POLY HISTORY [Read-only]
inchi -- InChI format
inchikey -- InChIKey [Write-only]
inp -- GAMESS Input
ins -- ShelX format [Read-only]
jin -- Jaguar input format
jout -- Jaguar output format [Read-only]
k -- Compare molecules using InChI [Write-only]
lmpdat -- The LAMMPS data format [Write-only]
log -- Generic Output file format [Read-only]
lpmd -- LPMD format
mae -- Maestro format
maegz -- Maestro format
mcdl -- MCDL format
mcif -- Macromolecular Crystallographic Info
MDFF -- MDFF format
mdl -- MDL MOL format
ml2 -- Sybyl Mol2 format
mmcif -- Macromolecular Crystallographic Info
mmd -- MacroModel format
mmod -- MacroModel format
mna -- Multilevel Neighborhoods of Atoms (MNA) [Write-only]
mol -- MDL MOL format
mol2 -- Sybyl Mol2 format
mold -- Molden format
molden -- Molden format
molf -- Molden format
molreport -- Open Babel molecule report [Write-only]
moo -- MOPAC Output format [Read-only]
mop -- MOPAC Cartesian format
mopcrt -- MOPAC Cartesian format
mopin -- MOPAC Internal
mopout -- MOPAC Output format [Read-only]
mp -- Molpro input format [Write-only]
mpc -- MOPAC Cartesian format
mpd -- MolPrint2D format [Write-only]
mpo -- Molpro output format [Read-only]
mpqc -- MPQC output format [Read-only]
mpqcin -- MPQC simplified input format [Write-only]
mrv -- Chemical Markup Language
msi -- Accelrys/MSI Cerius II MSI format [Read-only]
msms -- M.F. Sanner's MSMS input format [Write-only]
nul -- Outputs nothing [Write-only]
nw -- NWChem input format [Write-only]
nwo -- NWChem output format [Read-only]
orca -- ORCA output format [Read-only]
orcainp -- ORCA input format [Write-only]
out -- Generic Output file format [Read-only]
outmol -- DMol3 coordinates format
output -- Generic Output file format [Read-only]
paint -- Painter format [Write-only]
pc -- PubChem format [Read-only]
pcjson -- PubChem JSON
pcm -- PCModel Format
pdb -- Protein Data Bank format
pdbqt -- AutoDock PDBQT format
png -- PNG 2D depiction
pointcloud -- Point cloud on VDW surface [Write-only]
pos -- POS cartesian coordinates format [Read-only]
POSCAR -- VASP format
POSFF -- MDFF format
pov -- POV-Ray input format [Write-only]
pqr -- PQR format
pqs -- Parallel Quantum Solutions format
prep -- Amber Prep format [Read-only]
pwscf -- PWscf format [Read-only]
qcin -- Q-Chem input format [Write-only]
qcout -- Q-Chem output format [Read-only]
report -- Open Babel report format [Write-only]
res -- ShelX format [Read-only]
rinchi -- RInChI [Write-only]
rsmi -- Reaction SMILES format
rxn -- MDL RXN format
sd -- MDL MOL format
sdf -- MDL MOL format
siesta -- SIESTA format [Read-only]
smi -- SMILES format
smiles -- SMILES format
smy -- SMILES format using Smiley parser [Read-only]
stl -- STL 3D-printing format [Write-only]
svg -- SVG 2D depiction [Write-only]
sy2 -- Sybyl Mol2 format
t41 -- ADF TAPE41 format [Read-only]
tdd -- Thermo format
text -- Read and write raw text
therm -- Thermo format
tmol -- TurboMole Coordinate format
txt -- Title format
txyz -- Tinker XYZ format
unixyz -- UniChem XYZ format
VASP -- VASP format
vmol -- ViewMol format
wln -- Wiswesser Line Notation [Read-only]
xed -- XED format [Write-only]
xml -- General XML format [Read-only]
xsf -- XCrySDen Structure Format [Read-only]
xyz -- XYZ cartesian coordinates format
yob -- YASARA.org YOB format
zin -- ZINDO input format [Write-only]

Answer 2

Go here, no need to install, use on the web http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html