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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Received on Sun Aug 27 2006 - 06:07:22 PDT
