ADL: Differences betwn cluster and reference rmsd

mswingle at mswingle at
Tue Apr 21 01:15:46 PDT 2009

----- Original Message -----
From: Sharath Roy <royshari87 at>
Date: Tuesday, April 21, 2009 0:19 am
Subject: ADL: Differences betwn cluster and reference rmsd
To: autodock at

> Can some one tell the exact difference btwn Cluster and reference rmsd 
> obtained in the dlg file.....
> As far as i can see, cluster refers to the deviation among the cluster 
> itself i.e in a cluster, there will be different number of conformers 
> its the rmsd btwn any 2 among the same cluster...........

Cluster RMSD is calculated relative to the lowest energy conformation in the cluster (i.e. 
the lowest energy conformation would have a cluster RMSD of zero).

> One more Reference is probably there would be a seed conformer based 
> on which the the deviation in terms of other conformers is defined..........

Correct. By default, this is calculated relative to the coordinates given in the input pdbqt 
file (i.e. the file specified after the "move" keyword in the dpf file). You can specify a 
different reference conformation with the "rmsref" keyword.



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