ADL: NCI library in PDBQT library....

t.a.ruden at usit.uio.no t.a.ruden at usit.uio.no
Wed Jan 16 15:18:28 PST 2008


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



More information about the autodock mailing list