ADL: why cluster rmsd =0 ?

qiaoyan qiaoyan at dicp.ac.cn
Fri Mar 28 02:03:16 PDT 2008


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.  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 ?

Please help me.thank you !

 



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