[AMBER] Backbone Rmsd

From: jacob wick <jacobwick.la.gmail.com>
Date: Mon, 16 Mar 2015 22:17:46 -1200

Hi all,

The command for cpptraj

rms first out rna_run.rms .P,O3',O5',C3',C4',C5' time 0.50

gives a better converged value for the rmsd deviation.

Is this script helping in comparing backbone of reference with the backbone
of frames (without taking residues deviations in account) or it is
superimposing the reference backbone with the backbones of frame and giving
the deviations with respect to the residues?

Thanks and Regards,
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Received on Tue Mar 17 2015 - 03:30:02 PDT
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