VMD-L Mailing List

From: gurunath katagi (gurukatagi_at_gmail.com)
Date: Fri Dec 04 2009 - 00:20:03 CST

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