ADL: Differences betwn cluster and reference rmsd

mswingle at jaguar1.usouthal.edu mswingle at jaguar1.usouthal.edu
Tue Apr 21 01:15:46 PDT 2009


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


> 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 
> obtained......so 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.

Regards,

Mark


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