Re: [AMBER] j-restrained peptide

From: Rossella Noschese <>
Date: Mon, 22 Nov 2010 12:23:54 +0100

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??


2010/11/4 case <>

> 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
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