From: Jérôme Hénin (jerome.henin_at_uhp-nancy.fr)
Date: Tue Apr 25 2006 - 13:32:10 CDT
I am not an expert in SMD, but other methods could be useful. You might be
interested in a study we did recently about the dimerization of transmembrane
alpha-helical segments. We used NAMD to simulate both the association of
native proteins (ABF sampling) and the effect of point mutations (alchemical
The reference is:
J. Hénin, A. Pohorille and C. Chipot, J Am Chem Soc. 2005, 127(23):8478-84
See the abstract there:
I hope this gives you ideas about how some tools available in NAMD could be
applied to your problem.
Le Mardi 25 Avril 2006 18:24, L. Michel Espinoza-Fonseca a écrit :
> Dear all,
> We're trying to setup a SMD simulation of the dissociation of a
> monomer. I've been doing some research to see if somebody else has
> done that before, and I found an interesting study on insulin. The
> problem is that the authors use SMD to completely unfold the dimer.
> What we're trying to do is to create some mutants on our protein and
> then run SMD to see to what extent the mutations affect the stability
> of the dimer. We do *not* want to unfold the dimer. So, here's my
> question. Is there any way in which we can perform the SMD by pulling,
> let's say, the center of mass of one monomer?
> All suggestions are really welcome!!
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