Re: [AMBER] rmsd with fit

From: Daniel Roe <>
Date: Mon, 20 Jan 2014 20:08:33 -0700


On Mon, Jan 20, 2014 at 6:34 PM, Jio M <> wrote:

> 1) rms using nofit means it will NOT transform/translate and use simply
> formula as in wiki RMSD (v,w):


2) rms without nofit will perform transform/translate to get best fit
> (which is best minimum rmsd out of all transformations)

Also yes.

> Then in that case I would like to check if internal geometry was fixed
> (for 1-10) using EMAPs then I should get flat rmsd for 1-10 residue for
> whole simulation just by using:
> rms reference mass :1-10 out test.rms (as this should transformation to
> provide best fit)

Assuming your reference structure is the same as the one you started the
simulation with (i.e. is the structure with geometry you would like to
maintain), then yes. You could also use 'rms first' since you are holding
the geometry for that region fixed anyway.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Jan 20 2014 - 19:30:02 PST
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