Re: [AMBER] Structural alignment & RMSD calculation

From: Daniel Roe <>
Date: Tue, 8 Feb 2011 11:10:41 -0500


In order to get the RMSD of a specific region after fitting on another
region you need two rms commands. Say your reference is residues
1-100, and you want the rms of residues 50-55:

reference refstruct.rst7
rms reference :1-100
rms reference :50-55 nofit out rmsd.dat

The first rms command performs the best fit, then the second rms
command calculates the rmsd you want without changing the fit from the
first rms command.


On Mon, Feb 7, 2011 at 1:50 PM, Rahul Banerjee
<> wrote:
> Dear All,
> How can I calculate RMSD for a given region in the protein by aligning the core structure with a given crystal structure? I have made some changes in the protein (mutation) and due to that some loop regions are likely to become flexible. Where the core structure is unlikely to move. I have crystal structure of the mutated form as well, that I can use as reference in the alignment process.
> Thanking you.
> With best regards,
> Rahul
> _______________________________________________
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Received on Tue Feb 08 2011 - 08:30:02 PST
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