Re: RMSD for individual residue

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Mon Nov 30 2009 - 12:10:14 CST

Hi Gurunath,

The reason why you are getting different answers for the two methods
that you specify is that each chain in your complex is not going to be
synchronized with the other chains. Depending on the arrangement of
the chains, residue k in chain 1 is possibly in a different
environment as residue k in chain 2 (and is certainly undergoing
different stochastic motions as it collides with its neighbors and
solvent).

The method that you chose is up to you and will depend on what you are
actually interested in determining about your system.

Best wishes,
Josh

On Nov 30, 2009, at 12:55 PM, gurunath katagi wrote:

> Dear all,
> I am calculating the average RMSD over time of each residue in a
> protein molecule which has multiple chains (four ).(RMSD for
> individual residue using residue_rmsd.tcl)
> My question is whether we need to calculate the Average RMSD of each
> residue for each individual chain or take it has whole (four chains ).
>
> Because , when i did by both methods (taking the RMSD chain wise or
> as a whole), i am getting different RMSD values for each residue . I
> am not getting why there is a difference for individual residue and
> whether i need to take the RMSD for individual residue at once or
> chain wise ?
>
> Thank you
> Gurunath
>
>
> --
> Gurunath M Katagi
> Graduate Research Student
> Bio molecular computation Laboratory
> Supercomputer Education & Research Center
> Indian Institute Of Science, Bangalore- 560012
> Karnataka State, India
> Phone:080-22932737-319,080-22933061
> email: gurunath_at_rishi.serc.iisc.ernet.in
>

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