[Dock-fans] RMSD calculation

[John J. Irwin]

Hi Loraine

I believe this feature is available as "subtan" (shape Tanimoto) in the
ROCS package and the shape toolkit from OpenEye. I am sure there are
other programs that do this as well.

Good luck.

John


BRILLET Loraine 216515 wrote:
>
> Dear all,
>
>  
>
> I usually use VMD to calculate RMSD between docking pose and
> crystallized pose. But this program uses the atom numbering given in
> input mol2 or pdb file to align the 2 molecules or to calculate the
> RMSD. So, it doesn’t work properly if the atom numbering is not the
> same in the 2 files. I haven’t manage yet to overcome this problem.
>
>  
>
> I welcome any suggestion.
>
>  
>
> Does anyone know if one (free) RMSD calculator exists, which uses
> sub-structural search to align ligands and calculate RMSD?
>
>  
>
> Thanks for all the suggestions you could give me.
>
>  
>
> Regards,
>
>  
>
> Loraine
>
>  
>
>  
>
>  
>
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