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

Garrett M. Morris garrett at scripps.edu
Wed Mar 26 19:04:01 PDT 2008


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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