Re: [AMBER] Calculation of single atom radius of gyration

From: Jason Swails <>
Date: Wed, 24 Oct 2012 18:52:22 -0400

On Wed, Oct 24, 2012 at 5:50 PM, Amy Davenport <> wrote:

> > Hi,
> > I am trying to calculate the radius of gyration of single atoms in a
> protein molecule. I used the radgyr command in ptraj, but that seems to
> only allow for selection and calculation of radius of gyration from full
> amino acid residues.
> > For example, the command radgyr out radgyr_19N.dat :147 calculates the
> ROG for the entirety of amino acid 147.
> > However, radgyr out radgyr_19N.dat :10.NZ does not calculate only for
> the NZ atom, it returns all zeroes. Getting rid of the .NZ gives you the
> full residue calculation again.

Why do you expect the radius of gyration for a single atom to be non-zero?
 The center of mass of a single atom is that atom, and the distance between
an atom with itself is always zero.

You can check that ptraj will take any arbitrary mask by selecting 2 atoms
and calculating the radius of gyration of that selection (which will be


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Wed Oct 24 2012 - 16:00:03 PDT
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