On Wed, Oct 24, 2012 at 5:50 PM, Amy Davenport <adavenpo.ucsd.edu> 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
non-zero).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Oct 24 2012 - 16:00:03 PDT
