[AMBER] average structure with RMSF or RMSD?

From: newamber list <newamberlist.gmail.com>
Date: Wed, 17 Sep 2014 15:17:29 +0100

Hi All

I have seen papers and they report rmsd plot using average structure as a
reference but they dont mention how did they obtain average structure? I
also want to plot rmsd with average structure as reference.

In amber archive it has been suggested to do first RMSD fitting then
calculate average structure over msd fitted. Like this:

trajin md1.trj
rms first out rms.dat :1-100
average avg.pdb pdb

But which structure to be chosen as 'first' (let it be from some
equilibrated part?) or just I should use average without RMSD step:

trajin md1.trj
average avg.pdb pdb

Also as I googled some people use RMSF to get average strcutre.

I am not sure which is best/better way of considering average structure

Thanks for any suggestions
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Received on Wed Sep 17 2014 - 07:30:02 PDT
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