backbone restraints

From: Michael Zimmermann (
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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