Re: backbone restraints

From: Jérôme Hénin (
Date: Wed May 26 2010 - 14:47:13 CDT

Hi Michael,

You could setup an RMSD variable within the collective variables
module, and assign this variable an "upperBoundary" and an


On 26 May 2010 17:46, Michael Zimmermann <> wrote:
> Dear fans of NAMD,
> I have a pair of proteins that I would like to dock together, but three
> docking algorithms have now failed to meet known distance criteria for their
> interaction.  So, I am running SMD to pull the two into the "correct"
> position.  I have the larger of the two fixed in space with "fixedAtoms" and
> the other has the SMD force applied to it.  I plan to minimize the
> structures after this stage is complete to fix the side chains and the like.
> My question is whether or not I can also keep the backbone of the mobile
> protein rigid.  I don't want it to be spatially restrained (so not
> 'constraints' or 'fixedAtoms'), but I don't want the internal distances to
> change.  Is there an established way to do this?
> Thank you,
> --
> Michael Zimmermann
> Ph.D. student in Bioinformatics and Computational Biology
> Department of Biochemistry, Biophysics and Molecular Biology
> Iowa State University

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