ADL: generate pdbqt from pdb with metal
sargis at scripps.edu
Thu Mar 11 10:09:56 PST 2010
On 03/11/2010 02:23 AM, Paul Rigor (uci) wrote:
> Thanks! Is there an API to the underlying python modules so I can
> perform the conversion without using the gui?
There is currently no public API, but you can use obminimize  and
prepare_ligand to do the same thing.
I would recommend using 3D structures from PubChem, when available. For
some structures, such as sugar, I wasn't able to get the right 3D
coordinates with OpenBable energy minimization. 3D SDF from PubChem, on
the other hand, had the right 3D geometry.
Sargis Dallakyan, Ph.D. - Research Programmer
Department of Molecular Biology
The Scripps Research Institute
10550 North Torrey Pines Road, TPC-26
La Jolla, CA 92037-1000
Tel: (858) 784-9559
> On Wed, Mar 10, 2010 at 9:28 PM, <sargis at scripps.edu
> <mailto:sargis at scripps.edu>> wrote:
> > Hi,
> > I'm still having problems generating pdbqt from a pdb file. I've
> > 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
> 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:
> 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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