Re: [AMBER] rmsd with fit

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 20 Jan 2014 17:49:22 -0700

On Mon, Jan 20, 2014 at 4:46 PM, Jio M <jiomm.yahoo.com> 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.

-Dan 

-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Jan 20 2014 - 17:00:02 PST
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