[AMBER] RMSD vs RMSF vs nofit-RMSD

From: Nitin Sharma <sharmanitin.nus.edu.sg>
Date: Fri, 27 Dec 2013 01:40:05 +0800

Respected sir,

This might be very silly but I hope you can help me to clarify few things.

I know the definition of RMSD, RMSF and nofit-RMSD i.e. RMSD calculates the RMSD by fitting over the reference structure provided by the user. RMSF calculates RMSD but with respect to the average structure and nofit-RMSD calculates RMSD without fitting against the provided reference. Therefore the they give different results.

Now my question is what to use in which scenario? What is difference in application of the RMSD, nofit-RMSD and RMSF ?

What I should use when I want to see the influence of the mobility of particular residues on ligand binding interaction?

Thanks in advance.

Nitin Sharma
Department of Pharmacy,Faculty of Science,National University of Singapore,block S7, Level 2, Singapore : sharmanitin.nus.edu.sg<mailto:sharmanitin.nus.edu.sg> ; linkedin<sg.linkedin.com/in/imsharmanitin/>

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Received on Thu Dec 26 2013 - 10:00:02 PST
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