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

From: Daniel Sindhikara <>
Date: Fri, 26 Oct 2012 10:54:15 +0900

I think Jason mentioned this previously, but the radius of gyration of a
single point is always zero.
This is obvious from the definition of the radius of gyration.
Perhaps you trying to find something other than the radius of gyration
(such as the average distance between a single atom and the center of mass
of the protein?). In that case the dist command might be more useful than


On Fri, Oct 26, 2012 at 8:02 AM, 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.
> >
> > Any help would be greatly appreciated.
> > Amy Migliori, UCSD department of physics/biochemistry
> _______________________________________________
> AMBER mailing list

Dr. Daniel J. Sindhikara <>
Ritsumeikan University <> <>
AMBER mailing list
Received on Thu Oct 25 2012 - 19:00:04 PDT
Custom Search