Dear Charles,
Thanks a lot!! Now it works with keeping all clock atoms.
I would like to go back to your earlier suggestions: "properly include
solvent", "appropriate
temperature", and "how large an ensemble is needed for convergence". Could
you give me more details?
Besides, I took the "collapse" part off, because the calculated structure
would be "too compact" for a
denatured protein with it. Or I should keep it with better restraint setup?
#####
command("""
collapse
assign (resid 1:76) 25.0 15.0
scale 1.0
end
""")
#####
Best wishes,
Jie-rong
2008/4/25 <Charles at schwieters.org>:
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> Hello Jie-rong--
>
> >
> > If I took all SBMF mode out, the script goes well again! It might
> because of
> > the clock atom? However, I couldn't set it up properly. Since I only
> > recorded data in one spectrometer, I supposed that only one clock atom I
> > should add (e.g. 777 as in the example files); but how to have an proper
> > correspondence psf file as input for the clock atom? Thanks!!
> >
>
> you can keep the extra clock atoms- but make sure the coordinates are
> defined. I suspect that the NANs you were getting previously came from
> undefined clock atom coordinates.
>
> best regards--
> Charles
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