ADL: generate pdbqt from pdb with metal

Paul Rigor (uci) paul.rigor at uci.edu
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?

Paul

On Wed, Mar 10, 2010 at 9:28 PM, <sargis at scripps.edu> 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: http://www.youtube.com/watch?v=niw6gHDLfO4
>
> Resulting pdbqt (attached) seems to be all right.
>
> See also:
> http://pyrx.scripps.edu/blog/56-preparing-ligands-for-docking
>
> http://mgl.scripps.edu/forum/viewtopic.php?f=11&t=728&p=1174&hilit=+bond&sid=2faf41b1bbc94795a3e550d0a20725bb#p1174
>
>


-- 
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
http://www.ics.uci.edu/~prigor


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