Re: [AMBER] j-restrained peptide

From: case <>
Date: Wed, 3 Nov 2010 21:01:17 -0400

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 Wed Nov 03 2010 - 18:30:03 PDT
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