[Dock-fans] RMSD calculation

[Eric Pettersen]

> 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?

Chimera can't do substructure matching, but if the atom names in the  
two files correspond then Chimera will match them correctly  
regardless of the order in the file (use the "match" command).  I  
hope this helps.

--Eric


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu