ADL: generate pdbqt from pdb with metal
Paul Rigor (uci)
paul.rigor at uci.edu
Thu Mar 11 16:15:04 PST 2010
Thanks again Sargis,
Also, regarding PyRx's molecule import... Is it capable of reading a pdb
file with multiple models? I loaded a giant file (well 100+MB) which
contains over 1K structures... and it took a long time to load (almost 2
hours). After loading the file, it's "read test" states that there's "1
chain(s) with [93.5K] atoms". I know the pdb file is properly formatted.
I would like to extend PyRx for use with our SGE grid engine... aside from
looking into the code, do you have a proper documentation for extending
On Thu, Mar 11, 2010 at 10:09 AM, Sargis Dallakyan <sargis at scripps.edu>wrote:
> 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.
>  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.
> 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
>> 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
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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