AMBER Archive (2009)

Subject: Re: [AMBER] Fix the local structure as a rigid body

From: David A. Case (
Date: Tue Jun 16 2009 - 10:41:04 CDT

On Tue, Jun 16, 2009, Carlos Simmerling wrote:

> > I want to fix the local structure (12 to 15, and 18 to 20) as a
> > rigid body. Is my input file correct?
> >
> > restraintmask=’:12-15,18-20’,

Just to be clear: this restraintmask will keep the absolute positions of
residues 12-15 and 18-20 fixed. This of course will keep any secondary
structure in that region intact, but it will also fix the relative positions
of residues 12-15 with respect to residues 18-20. If that is what you want,
you should be OK.


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