ADL: RMSD reference

[Gav]

Ruth Huey wrote:
> Hi,
> 
> -In AutoDock, conformational clustering is performed after all the 
> dockings have finished if the keyword |analysis| is given in the docking 
> parameter file (DPF).
> -By default,  the atoms in the moving ligand (defined by the |move| 
> keyword in the DPF) are used in the RMSD clustering calculations based 
> on the tolerance defined by the |rmstol| keyword in the DPF.
> -If the |rmsref |keyword is in the DPF, the coordinates of the atoms in 
> that file are used instead. Consequently, the file specified by the 
> |rmsref |keyword must contain the same atoms in the same order as the 
> file specified by the |move| keyword.
> -If the docking includes flexible residues, by default only the atoms in 
> the moving ligand are used for the rmsd calculation.  If the |rmsatoms 
> |keyword  is included in the DPF, the coordinates of the atoms in the 
> flexible residues are also used for the rmsd calculation. In that case,  
> the file specified by the |rmsref |keyword must also contain the 
> flexible residue atoms in the same order as the file specified by the 
> |flexres| keyword.
> 
> Please note that the rmsd calculation in AutoDock uses the distances 
> between each atom in the docked structure and the nearest atom of the 
> same element in the reference structure (instead of the distance between 
> each atom and its equivalent in the reference structure) unless the 
> |rmsnosym |keyword is in the DPF.
>     Ruth
> 
> Isabel Hilligerk wrote:
>> Hi,
>>
>> Thank you for your previous help. I'm interested in reporting the 
>> results i
>> have obtained with AutoDock. It seems that the RMSD reference value is an
>> interesting value to report because it indicates the success of the 
>> docking
>> process. I would be very thankful if someone could explain me the use 
>> of the
>> rmsref command. I also want to know which is the default reference
>> estructure used for the RMSD reference calculation when i haven't 
>> specified
>> any molecule.
>>
>> Regards,
>>
>> Isabel Hilliger.
>> ________________________________________________
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>>   
> 
> ________________________________________________
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> 
AHH!

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