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.

  • 3
    $\begingroup$ If you need support with the program, you probably should file a bug report/issue or ask their mailing list. $\endgroup$ – Martin - マーチン Apr 16 at 23:30
  • $\begingroup$ @Martin-マーチン - indeed. I'd guess this is a very old version of Open Babel. $\endgroup$ – Geoff Hutchison Apr 19 at 16:26

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


# 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]
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
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]

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

  • 1
    $\begingroup$ +1 and welcome to our new community! Thank you for your contribution and we hope to see much more of you in the future!!! However can you please try to expand this answer a bit and make it look a bit less like a "link-only answer"? In fact, you telling us to "go here", make this look like it's a spam link. $\endgroup$ – Nike Dattani Apr 21 at 2:36

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.