ADL: generate pdbqt from pdb with metal

Sargis Dallakyan 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 [1] and 
prepare_ligand to do the same thing.

[1] http://openbabel.org/wiki/Obminimize

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.

Bests,
Sargis

-- 

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
http://mgltools.scripps.edu/Members/sargis


> Paul
>
> 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
>     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
>     <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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