ADL: Unable to assign MAP type to atom As and Xx

Stefano Forli forli at
Tue Sep 28 19:38:50 PDT 2010

Hi He,

I suggest you to use the NCI diversity set II from the ZINC database that's filtered for 
unusual atom types (like As) for which AutoDock doesn't have parameters, and it's already 
available as Mol2.
In this way you should be able to avoid these problems.

Otherwise, you should manually filter these ligands and remove them before generating the 
PDBQT files.

Hope this helps,


He demeatry wrote:
>  Dear:
> I am using autodock4 for virtual screening against NCI diversity set II. I
> download the SDF format of diversity set II and convert it to mol2 format
> using Openbabel 2.2.3. However, when I was processing mol2 to pdbqt, the
> message shew it unable to assign MAP type to atom As and Xx (some ligands
> contains atom As or Xx), because there are no Gasteiger parameters available
> for such atoms. NCI diversity set I does not have such phenomena. How can I
> solve the problem?
> Thanks a lot!

  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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