Re: [AMBER] Multiple restraint masks

From: Jason Swails <>
Date: Tue, 26 Nov 2013 11:29:42 -0500

On Tue, Nov 26, 2013 at 10:34 AM, Michael Garton <
> wrote:

> Dear all,
> Is it possible to employ multiple restraint masks within the same
> simulation? For instance, if one has a protein with three domains and you
> wish to restrain a subset of atoms within each of these domains, can you
> restrain each subset independently so that inter-subunit motion is not
> affected?

Positional (cartesian) restraints do not work this way. These restraints
do not work in internal coordinates as you would seem to like. They act by
'anchoring' the system into a particular (arbitrary) point in space. You
would need restraints that act via internal coordinates in order to fix
relative particle orientations without affecting other particle-particle
orientations. You would need to use distance, angle, and/or torsion
restraints to fix relative orientations, although it would require a large
number of restraints to implement an internal coordinate-equivalent of
positional restraints. (Chapter 6 in the Amber manual describes how to set
up distance/angle/torsion restraints.)


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Nov 26 2013 - 08:30:03 PST
Custom Search