AMBER: atomifluct

From: Miguel Ferreira <tetrass.hotmail.com>
Date: Fri, 25 Aug 2006 11:09:03 +0000

Dear amber users,


I want to calculate the RMSF for backbone atoms of my protein. I read that
it is better to do a RMS fit to the average structure prior to do the
atomifluct. However I am not sure if it is also better to first center the
solute and image the system...I wonder if someone could tell me if my script
is correct:

trajin md2.mdcrd
reference average_struct.pdb
rms reference mass out backbone_mass_reference.rms .N,CA,C time 0.2
atomicfluct out back_atomicflubfactor.apf .C,CA,N byres bfactor

Thanks in advance
Miguel



Could someone please tell me if is this correct?

_________________________________________________________________
MSN Hotmail, o maior webmail do Brasil. http://www.hotmail.com

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Aug 27 2006 - 06:07:22 PDT
Custom Search