ADL: reference RMSD

Óscar VIllacañas Pérez ovillacanas at
Wed Jan 30 10:16:48 PST 2008

Dear Dario,

AutoDock4 looks for symmetric parts within the ligand and then performs
(I think) all possible superimpositions and computes respective RMSDs.
The 'Reference RMSD' is then the lowest value. Does your script
considers symmetry within ligand?


El dl 28 de 01 del 2008 a les 17:08 -0500, en/na Dario Ghersi va
> 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  
> 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
> 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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Óscar Villacañas Pérez
Intelligent Pharma
T. +34 934 034 551

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