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.

Just FYI!

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
PyRx?

Thanks,
Paul

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 [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
>>
>
>


-- 
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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