backbone restraints

From: Michael Zimmermann (michaelz_at_iastate.edu)
Date: Wed May 26 2010 - 10:46:09 CDT

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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