ADL: NCI library in PDBQT format....

Jack Shultz jackygrahamez at gmail.com
Mon Jan 21 16:33:20 PST 2008


I'll give you my two cents worth. I setup an automated script on my site
that downloads mol2 files from NCI cact
http://129.43.27.140/ncidb2/

Using the mol2 files as ligands, I use a binary port of the prepare_ligand4
with the following command line flag
 -l nsc1.mol2
With a standard ADT install you should be able to download that file and run
pythonsh prepare_ligand4.py -l nsc1.mol2
You can send me one of your files and I can see if I can get it working with
ADT.

Jack
On Jan 20, 2008 4:21 PM, <t.a.ruden at usit.uio.no> wrote:

> Hi!
>
> Sorry if my question is dumb, but I'm a newbie to this. It is also a
> rather lengthy intro, so bear with me please.
>
>
> I downloaded and installed AD4 and ADT 1.4.6. Then I proceeded to the
> task: running some screening calculations against the NCI library.
>
> I found the NCI library in PDBQ format (which I understand is AD3 format
> of ligands). However, trying to convert it into PDBQT format, using
> pdbqtopdbqt.py in ADT, I ran into several problems. One is apparently
> linked to the known problems (documented in
>
> http://autodock.scripps.edu/faqs-help/how-to/how-to-prepare-a-ligand-file-for-autodock4
> )
> Although I use ADT version 1.4.6 I still get the error:
> ERROR: All ATOM and HETATM records must be given before any nested
> BRANCHes
>
> Now I got around this by using ADT by hand on one ligand, converting pdbqt
> to pdb (using pdbqttopdb.py in adt), and then prepare_ligand4.py on the
> pdb files. Scripting this however I got into a mess, since atom-types
> seems to be very different from AD3 to AD4 (f -> F, c -> CL...).
>
> I tried to sed (or query-replace if you like) my way out of this, but
> without any luck at this stage.
>
> So I have three questions:
> 1.) Does anybody have any input on ho to get a working NCI-library? Maybe
> someone has a working NCI-library in PDBQT format for instance (you will
> be acknowledged for your effort :-))?.
> 2.) In the pdb generated from adt, there is a dive-keyword. What is this,
> and what is the format?
> 3.) Is there an overview of the names of atoms in AD4. It says on the web
> that it uses atom symbols, but I get complaints about As. I thought As was
> correct. Also I get confused since it seems to use Br and CL. But then
> again I'm just a theoretical chemist, so I get easily confused ;-).
>
> ----
>
> I appreciate *any*input on the subject.
>
> best
> Torgeir
>
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