Re: [AMBER] rmsd with fit

From: Jio M <>
Date: Mon, 20 Jan 2014 17:34:23 -0800 (PST)

Dear Daniel and Wei

Thanks, but I am lost somewhat I think...

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)

am I right?

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)


On Tuesday, January 21, 2014 12:49 AM, Daniel Roe <> wrote:
On Mon, Jan 20, 2014 at 4:46 PM, Jio M <> wrote:

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

FYI 'fit' is not a valid keyword for the 'rms' command in either ptraj or
cpptraj. As Wei mentioned the default behavior of 'rms' in both programs is
to calculate the best-fit RMSD. The 'nofit' keyword means do not perform
any fitting; the RMSD is calculated between the target and reference
structures as they are.


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 - 18:00:02 PST
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