VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 09 2009 - 00:25:01 CST

Hi,
  I'm having a hard time following a couple of the details you
listed below as some of the statements you make lack details.
Are the RMSD values you calculated _exactly_ equal,
or just very close to the same? If they are _exactly_ equal, I would
question whether your atom selections were correctly selecting
the different chains. You can determine if you're getting the
right atoms selected by querying the atom indices associated with
each selection and confirming that you're actually getting different
atom indices for the different chain selections as appropriate.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Dec 04, 2009 at 11:50:03AM +0530, gurunath katagi wrote:
> Dear all,
> The protein on which i have done a simulation is a tetramer and i need to
> find the RMSD for individual residues of all chains in the proteins.
> The namd tutorial on ubiquitin has discussed this for a protein which has
> a single chain.
> Now I wanted to know whether i can apply to this tetramer...
>
> Because I have made the atom selection for individual chains and done
> the RMSD calculation as for the ubiquitin , but RMSD is equal for all
> chains.
> I am not getting why the RMSD is coming equal. or should i modify the
> script so that it works for tetramer or should i calculate the rmsd for
> all chains at once as done for the ubiquitin ? or is there any other
> strategy.
>
> Can any one suggest me how to go about this.
>
> --
> 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 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078