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

From: Daniel Roe <>
Date: Wed, 24 Oct 2012 18:51:46 -0400


Currently the radius of gyration command calculates the RoG of all
atoms in mask to the center of mass (or geometric center) of the atoms
in that mask, so if only one atom is selected it's the distance of
that atom to itself which is of course zero. I think you can get what
you want by just using the distance command. For example, if your
solute is residues 1 to 12 and you want the distance of atom NZ in
residue 10 from the center of mass of the solute:

distance :10.NZ :1-12

Hope this helps.


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.
>> Any help would be greatly appreciated.
>> Amy Migliori, UCSD department of physics/biochemistry
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
AMBER mailing list
Received on Wed Oct 24 2012 - 16:00:02 PDT
Custom Search