Re: [AMBER] Applying nmr restraints: Radius of gyration or COM distance for large groups of atoms

From: Jason Swails <>
Date: Thu, 09 Jan 2014 10:33:34 -0500

On Wed, 2014-01-08 at 15:15 -0600, Nihal Korkmaz wrote:
> Dear Amber community,
> My aim is to apply radius of gyration/COM distance restraints into my
> simulations. The goal is to maintain my protein extended conformation.
> I'd greatly appreciate any comments and suggestions please.

The only way to apply radius of gyration restraints to your system is to
use the NCSU modules in sander. Otherwise, you can try to impose a
distance restraint between the first and last residues of your chain and
define the flat-well potential to penalize only those distances that
fall below a certain cutoff. You can accomplish this by setting the
force constant for the 'right' half of the flat-well to 0 (rk3, I

The Amber manual has a good description of defining the NMR restraint


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Jan 09 2014 - 08:00:02 PST
Custom Search