Re: [AMBER] rmsd

From: David Case <>
Date: Tue, 28 May 2019 01:49:22 +0000

On Mon, May 27, 2019, Hirdesh Kumar wrote:
>I have simulated a dimer (A: 1-370, B: 371-540)
>Now, I want to study the motion of 1 monomer with respect to the second
>parm mol.parm
>#align to first frame, backbone atoms
>reference :1:1-370.CA,N,C,O
>rms ref out rmsd.dat :1-370.CA,C,N,O
>rms ref out rmsd.dat :371-540.CA,C,N,O

You probably want to add the "nofit" keyword to the final rms command.
The first rms command will align monomer A to the reference. Then the
second command (adding in "nofit") will compute how far monomer B has
moved away from the reference state, without doing any fitting (since
alignment was already done with the first rms command.)

...good luck....dac

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Received on Mon May 27 2019 - 19:00:02 PDT
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