ADL: Use crystal structure with ligand as reference for docked ligands?

Bjoern Olausson olausson at gmail.com
Thu Mar 27 10:10:11 PDT 2008


I am not shure I did understand what you wrote.

What I think I understood was:

- Extract the complexed ligand from the mol2 file and write it in a
new mol2 file.
- Use AutoDockTools to open the mol2 file and save it as pdbqt (lets
say ref.pdbqt)
- add "rmsref ref.pdbqt" to the option in the .dpf file (or
prepare_dpf4.py -l $ligand.pdbqt -r $receptor.pdbqt -p
rmsref=ref.pdbqt)

Would that be correct?

But when I understand it right, it will just check the konformation,
not the position in the protein. So when two conformations fit
exactly, but are found in two different places I would get a perfect
RMS, wouldn't I?

If that is right, is there another method except
- writing out the "AutoDocked" complex
- align the macro molecules from "AutoDocked complex" and "complexed
crystal strukture" (they should fit 100%)
- then check the RMS for the docked ligand

In this way I could either check the RMS for the ligand  konformation
or the RMS for position of the ligand  in the macro molecule

But this is rather "unpleasant" for 50 or more konformations ;-)

Thanks for your help, and suggestions  really appreciate  it.

kind regards
Bjoern

On 3/27/08, Garrett M. Morris <garrett at scripps.edu> wrote:
> Dear Bjoern,
>
> On 26 Mar, 2008, at 5:14 pm, Bjoern Olausson wrote:
> > Hi community,
> >
> > I am new to AutoDock and trying to validate this method for my needs.
> >
> > The dockings are working fine and everything seems fine.
> >
> > But how do I get a RMS?
> >
> > - Got a crystal structures from a protein as apo-protein and
> > complexed with a
> > ligand.
> >
> > - Docked the same ligand as found in the complexed crystal structure
> > into the
> > apo-enzyme
> >
> > - Analyzing the results shows a big cluster (35/50)
> >
> > But how do I set/select the ligand from the complexed structure as
> > reference
> > to calculate the RMS?
> >
> > Should I run the docking with the complexed structure? If thou, what
> > to do
> > with the ligand in the structure? Dos it interfere with the docking
> > process?
> >
> > I could not find a thing about the RMS in the FAQs and or tutorials.
> >
> > All in all, I just want to know if it is possible to use a crystal
> > structure
> > with a ligand as reference for my "AutoDocked" ligands.
> >
> > Any hint/tip is wellcome
>
>
> In AutoDock, you can use the "rmsref" command, which expects the name
> of the ligand PDBQ (AutoDock 3) or PDBQT (AutoDock 4) file as the
> argument.  Just give the filename of the crystallographic ligand
> coordinates in the appropriate format (PDBQ for AD3, PDBQT for AD4).
> Then if you read the AutoDock log file ("DLG") in a text editor, for
> example, you will see the RMSD to reference structure reported, under
> the RMS TABLE's "Reference RMSD" column:
>
>      RMSD TABLE
>      __________
>
> _____________________________________________________________________
>       |      |      |           |         |                 |
> Rank | Sub- | Run  | Binding   | Cluster | Reference       | Grep
>       | Rank |      | Energy    | RMSD    | RMSD            | Pattern
> _____|______|______|___________|_________|_________________|___________
>     1      1      7       -8.01      0.00      2.85           RANKING
>     1      2      1       -7.85      0.49      2.98           RANKING
>     1      3     10       -7.60      1.83      3.32           RANKING
>     1      4      3       -7.06      1.79      2.86           RANKING
>     2      1      5       -7.81      0.00      3.11           RANKING
>     2      2      4       -7.39      1.38      3.01           RANKING
>     2      3      9       -7.18      1.30      3.19           RANKING
>     2      4      6       -7.17      1.09      2.91           RANKING
>     3      1      2       -7.74      0.00      1.10           RANKING
>     3      2      8       -6.71      1.51      0.49           RANKING
> _______________________________________________________________________
>
>
> ADT should also show this information if you click on the "&" button
> in the Conformation Player widget.
>
> I hope this helps,
>
> G.
>
> >
> >
> > Thanks and regards
> > Bjoern
> >
> > --
> > There is nothing in this world
> > that does not have its decisive moment.
> >
> > Henri Cartier-Bresson
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> > ---
>
> ___
> Dr Garrett M. Morris, M.A. (Oxon.), D.Phil. (Oxon.)
>
> The Scripps Research Institute,       tel: (858) 784-2292
> Dept. Molecular Biology,  MB-5,       fax: (858) 784-2860
> 10550  North Torrey Pines Road,       email: garrett at scripps.edu
> La Jolla,  CA 92037-1000,  USA.       mgl.scripps.edu/people/gmm
>
>
>
>
>


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