From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed May 26 2010 - 14:47:13 CDT
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 <michaelz_at_iastate.edu> 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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