yes, we do this very often. the important thing is to be aware of the effect
of fitting. for example, it's best to fit the entire protein and then do
RMSD for each residue without refitting. if you fit each residue before
calculating the rmsd, the result is less meaningful.
On Fri, Mar 19, 2010 at 4:21 PM, Jio M <jiomm.yahoo.com> wrote:
> Dear AMBER users,
>
> I have a general query regarding RMSD... why we not carry out rmsd on
> residue basis e.g. on per amino acid basis. (sorry if same discussion had
> been occurred earlier)
>
> I mean to say, RMSD is ''sort of averaging'' out the things as it is being
> divided by n number of atoms. So if (less or more) number of atoms are much
> deviated then it might not be clear (that is we can miss that deviation of
> atoms) from whole protein rmsd comparison.
>
> It can easily be determined on basis on per amino acid basis rmsd
> comparison or we can say on small number of atoms say 10 (obviously more
> less number of atoms being considered more exact we will reach). It will
> help to know which group is exactly responsible for variation even if it was
> not seen for WHOLE protein rmsd calculation (being averaged out)
>
> hope it is clear.
>
>
> thanks and regards,
>
> JIomm
>
>
>
>
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Received on Sat Mar 20 2010 - 10:00:03 PDT
