ADL: generate pdbqt from pdb with metal

Paul Rigor (uci) paul.rigor at
Thu Mar 11 02:23:10 PST 2010

Thanks!  Is there an API to the underlying python modules so I can perform
the conversion without using the gui?


On Wed, Mar 10, 2010 at 9:28 PM, <sargis at> wrote:

> > Hi,
> >
> > I'm still having problems generating pdbqt from a pdb file.  I've
> included
> > a
> > sample compound from the Maybridge fragment library both the pdb
> > (converted
> > from sdf using babel) and the pdbqt generated by the ATD script.
> >
> > As you can see, the conversion is failing...
> ADT computes bonds based on how far atoms are from each other. The reason
> for this problem is that in the input (2D) structure (Z=0.000) atoms are
> too close to each other.
> I just did energy minimization using Open Babel widget in PyRx as
> described here:
> Resulting pdbqt (attached) seems to be all right.
> See also:

Paul Rigor
Pre-doctoral BIT Fellow and Graduate Student
Institute for Genomics and Bioinformatics
Donald Bren School of Information and Computer Sciences
University of California, Irvine

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