On Wed, Oct 06, 2010, Olivier Julien wrote:
>
> I am pursuing the structure determination of a DNA duplex
> dodecamer by NMR. I am comparing a DNA duplex containing a modified base,
>
> QUESTION #1:
> I am using the following backbone dihedral angles typical for B-DNA (+/- 40 degrees):
> (Bax et al., 1DUF.pdb)
> $alpha = -61; $beta = 180; $gamma = 57;
> $delta = 123; $epsi = -169; $zeta = -91;
> Does this seem appropriate?
I don't know. It depends on how many "real" NMR constraints you have and what
you want to do with the structrual ensemble once you get it.
> More importantly, how are the dihedral angles defined? Between -180 to
> +180? between -360 to +360?
It doesn't matter...dihedral angle is periodic, giving the same structure
every 360 degrees.
> Would -60 = 300 degrees?
Yes.
> If one look at http://ambermd.org/tutorials/advanced/tutorial4/files/5col.bb
> Is 2 CYT EPSILN -240.0 10.0 = -115 +/- 125 ?
Yes.
>
> QUESTION #2:
> Should I do a minimization after? Or is this sufficient?
You have already cooled (as I understand it) to a very low temperature.
Minimization probably won't change things very much, but you could try it to
see.
....dac
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Received on Thu Oct 07 2010 - 05:00:03 PDT
