[AMBER] Problem related to the RMSD and Atomic fluctuation

From: Sindrila Dutta banik <sindrila.duttabanik.yahoo.com>
Date: Sun, 17 Jul 2011 09:32:06 +0530 (IST)

Dear all,
I want to know what is the difference between the RMSD and atomic fluctuation computated by the 'AMBER'. I want to know the mathematical equation which is used to compute the two different variables.
I have few more questions related to RMSD.
(i) If I want to compute the RMSD of all non-hydrogen atoms what command shall I use. I am using "rmsd first mass out all.rms :1-420" command. But I think this command computes all atoms including hydrogen. [Note my system composed by 420 residues]
(ii) In my case the protein is composed by four domains. My result shows that the RMSD of overall protein is greater than RMSD of all individual domains. Is it possible and physically meaningful?  
With Best regards
AMBER mailing list
Received on Sat Jul 16 2011 - 21:30:02 PDT
Custom Search