ADL: reference RMSD

Ruth Huey rhuey at scripps.edu
Wed Jan 30 10:36:04 PST 2008


Dario Ghersi wrote:
> Dear all,
>
> I have a problem with the reference RMSD that's reported in the .dlg  
> file.
> If I compare that value with the one that comes out of  
> summarize_results4.py I get different values (sometimes the difference  
> is > 2.0A). I also calculated the RMSD separately with my script and  
> the results are consistent with summarize_results4.py.
> So I was wondering how the reference RMSD is actually calculated in  
> the .dlg file.
>
> Thank you very much,
>
> Dario Ghersi
> ________________________________________________
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>
>   

In the .dlg file, the rmsd calculation matches each atom in the docked 
structure with the closest one of the same atom type in the reference 
structure.
The python script matches each atom in the docked structure with its 
position in the reference structure.

   Ruth


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