Re: [AMBER] rmsd with fit

From: 126 <>
Date: Tue, 21 Jan 2014 07:57:06 +0800

Hi Joim,

nofit is not default.
In your case, you should do following command:

rms reference mass :1-10
#this will transform the structure based on 1-10
rms reference mass :11-20 out test.rms nofit
#this will calculate the rmsd

Hope this helps.


Wei Ye
PhD Candidate
Department of Bioinformatics and Biostatistics,
School of Life Science and Technology,

2014-1-217:46Jio M <> д

> 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
> thanks
> Jiom
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Received on Mon Jan 20 2014 - 16:00:05 PST
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