AMBER Archive (2006)

Subject: AMBER: atomifluct

From: Miguel Ferreira (tetrass_at_hotmail.com)
Date: Fri Aug 25 2006 - 06:09:03 CDT

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?

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