On Wed, Aug 11, 2010, Andrew Olson wrote:
> I have a question regarding NMR refinement. Is it common to see an
> increase in backbone RMSD in going from structure determination to after
> water refinement? After structure determination using CYANA my backbone
> RMSD is .27 A, but after water refinement is .55 A. I realize this
> isnt a big deal since .55 is still really tight but i was just curious
> if this is common? My force constants for dihedral angles are 50 and
> distance restraints is 20. I am asking because i notice that other
> papers that use the CYANA and AMBER combo have really low RMSD (.25-.40)
> while having nearly the same number of restraints. Just making sure my
> method is proper.
I think this is a common observation: inclusion of solvent effects (and other
parts of force fields taht get involved in refinement) tend to expand the
range of energetically favorable strutures that approximately satisfy the NMR
restraints. If you haven't done so already, you might look at this (somewhat
old!) paper:
%A B. Xia
%A V. Tsui
%A D.A. Case
%A H.J. Dyson
%A P.E. Wright
%T Comparison of protein solution structures refined by molecular dynamics
simulation in vacuum, with a generalized Born model, and with explicit water
%J J. Biomol. NMR
%V 22
%P 317-331
%D 2002
....dac
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Received on Fri Aug 13 2010 - 05:00:04 PDT
