ADL: ADT problem

Stefano Forli forli at
Wed Nov 2 11:55:41 PDT 2011

Hi Phil,

the correct procedure for preparing a PDBQT file is the following:

-read the molecule;
-Edit->Add Hydrogens [don't change the default values]
-Grid->Macromolecule...-> Choose

At the end, you will be prompted to save your file.
The last step will perform automatically charge assignment (Gasteiger), non-polar 
hydrogens merge, AutoDock atom typing.

For further details on the procedure, please refer to the user guide:


On 11/02/2011 05:04 AM, Cunningham, Phil wrote:
> Hi Autodock
> I have a pdb file I wish to convert to pdbqt format using ADT
> I read in the molecule circa 4000 atoms
> edit misc - check missing atoms  says 0 (zero)
> edit hydrogens add polar only
> edit charges add Kollman
> edit charges compute Gasteiger - total charges added 6.0125
> edit charges check totals on residues spread charge over all atoms
> file write PDBQT  OK
> ERROR Cannot create the PDBQT file, all atoms do not have an
> autodock_element field
> can anyone point to my error?
> both RasMol and Jmol can display / interact reasonably with the source file
> babel / open babel blows up in windows and is taking an eternity on
> ubuntu (getting nowhere)
> many thanks
> phil

  Stefano Forli, PhD

  Research Associate
  Olson Molecular Graphics Laboratory
  Dept. Molecular Biology,  MB-112
  The Scripps Research Institute
  10550  North Torrey Pines Road
  La Jolla,  CA 92037-1000,  USA.

     tel: (858) 784-2055
     fax: (858) 784-2860
     email: forli at

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