ADL: why cluster rmsd =0 ?

Garrett M. Morris garrett at scripps.edu
Fri Mar 28 11:38:07 PDT 2008


Dear Qiayan,

On 28 Mar, 2008, at 2:03 am, qiaoyan wrote:

> Hello ,
>
> I am working on GPCR for my bachelor's thesis, I use autodock4  to do
> experiment  on PDBID-2RH1 beta2 ,first I remove the ligand carazolol  
> from
> the receptor ,then I dock them. .but the cluster rmsd is 0.

You have no clustering: it looks like you did 10 runs, but your  
conformations did not cluster at the "rmstol" value you specified.

The first member of every cluster has an RMSD of 0 Angstroms, since by  
definition it is the seed for the whole cluster.

To see clustering, you should try increasing the RMS tolerance value  
(using "rmstol").


>  I don't know
> why ,the dlg file is as follows:
>
>
>
>    RMSD TABLE
>
>    __________
>
>
>
> _____________________________________________________________________
>
>     |      |      |           |         |                 |
>
> Rank | Sub- | Run  | Binding   | Cluster | Reference       | Grep
>
>     | Rank |      | Energy    | RMSD    | RMSD            | Pattern
>
> _____|______|______|___________|_________|_________________| 
> ___________
>
>   1      1      6      -20.07      0.00      9.30           RANKING
>
>   2      1      3      -18.28      0.00     15.61           RANKING
>
>   3      1      4      -17.70      0.00     14.47           RANKING
>
>   4      1     10      -17.63      0.00     13.46           RANKING
>
>   5      1      1      -17.19      0.00     15.51           RANKING
>
>   6      1      2      -17.15      0.00     14.40           RANKING
>
>   7      1      5      -16.70      0.00     16.43           RANKING
>
>   8      1      7      -16.69      0.00     14.49           RANKING
>
>   9      1      8      -15.99      0.00     19.84           RANKING
>
>  10      1      9      -15.22      0.00     16.79           RANKING
>
> Another question:
>
> How to save the docked conformation as pdb ?

Two options:

(1) In ADT, use Analyze > Clusterings > Show, click on a bar in the  
histogram to bring up the Conformation Player widget, then click on  
the "&" button in the CP widget; finally, click "Write Complex" for  
the current conformation you are displaying.

(2) See the FAQ (frequently asked question):

http://autodock.scripps.edu/faqs-help/faq/is-there-a-way-to-save-a-protein-ligand-complex-as-a-pdb-file-in-autodock

I hope this helps,

Garrett

>
>
> Please help me.thank you !
>
>
>
> ________________________________________________
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> ---

___
Dr Garrett M. Morris, MA (Oxon), DPhil (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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