Hello dac, can you help me one more time?
I calculated my new coefficients (rjcoeff) that are directly related with
the dihedral phi, without passing through the addition of 60° (that was
necessary both for Pardi and for Amber default coefficients). I run the
simulated annealing with these new coefficients. The resulted final j is
what I expected for VAL (j=7.6), and it gives the right dihedral on my pdb!!
However, all the runs I made can never reach the target j value for ILE
(final j=9.1, target j=8.1). I tried with lots of different rk value and
this worked well for reaching the right value for VAL, but not for ILE... Is
there some flags or some refinements I can add to drive my calculation to
the desired value also for ILE??
Thanks!
2010/11/4 case <case.biomaps.rutgers.edu>
> On Wed, Nov 03, 2010, Rossella Noschese wrote:
> >
> > sorry I wasn't very clear in my second question. It may be a trivial
> > question...however, in my second run, I had, for example, for VAL an
> output
> > of j=7.6Hz (that was very near to my observed averaged j). This
> corresponds
> > to a dihedral phi of about -85°. But when I measured it on my pdb it was
> > about -145°. I believe that this means that I am measuring theta (85+60)
> not
> > phi. Therefore, there is something wrong, if I am measuring a j which
> should
> > give me a phi of 85°, yet I am calculating 145.° Could it be related to
> the
> > j being averaged or not ? I assumed that the j in the output is not
> > averaged, but is precisely related to the "final" molecule, therefore, it
> > should be the precise conformation with that dihedral angle.
>
> You should do a one-step minimization, to be sure that the value calculated
> is what you want. I think (but it has been a long time) that the Karplus
> coefficients need to be in terms of the H--H torsion angle, *not* some
> conventional backbone torsion. That is, the angle "tau" on p. 181 is the
> HN-N-Ca-Ha torsion, and the Karplus coefficients have to be written for
> that
> torsion. So make sure that with a known structure, you are getting the
> desired coupling constant.
>
> ...good luck...dac
>
>
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Received on Mon Nov 22 2010 - 03:30:03 PST
