[AMBER] rmsd with fit

From: Jio M <jiomm.yahoo.com>
Date: Mon, 20 Jan 2014 15:46:46 -0800 (PST)

Dear All

I have some query about rmsd calculation. If I just translate/transform coordinates of some structure (keeping internal coordinates same) then calculating like this does not make sense?
(In brief I have residues 1 to 20 and I simulated keeping 1-10 residues with fixed internal geometry, rigid body, using EMAP)

rms reference mass :1-10 out test.rms

this will give wrong impression that structure has changed much though it just translated

to avoid this do I need to use like this or something else?

rms reference mass :1-10 out test_fit.rms fit

(I used ''fit'' here and I think nofit is default)

But using fit gives same output (test.rms and test_fit.rms are same). I mean using fit rms graph should be almost flat

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Received on Mon Jan 20 2014 - 16:00:04 PST
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