Re: [AMBER] j-restrained peptide

From: Rossella Noschese <>
Date: Thu, 2 Dec 2010 10:30:13 +0100

Dear Case, I've also made simulations changing the distance restraints
relative to ILE, but nothing to do!! It seems that that target j value can't
be reached. Is it possible?

2010/11/22 Rossella Noschese <>

> 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 <>
> 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 Thu Dec 02 2010 - 02:00:02 PST
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