ADL: Unable to assign MAP type to atom As and Xx
forli at scripps.edu
Tue Sep 28 19:38:50 PDT 2010
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
Hope this helps,
He demeatry wrote:
> 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
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 scripps.edu
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