ADL: NCI library in PDBQT format....

Torgeir Andersen Ruden t.a.ruden at usit.uio.no
Thu Jan 24 00:23:28 PST 2008


Ahh, very good. I didn't get the mol2 files to work, but using pdb-files 
it worked perfectly (or at least as good as the Autodock release of NCI 
says it works).

Thank you very much.

best
Torgeir

Jack Shultz wrote:
> 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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