Thanks for the input, it was very helpful.
I'd like to extend this discussion a bit if that's alright. I've
noticed in several papers that people translate j-coupling values into
dihedral restraints in an effort (presumably) to avoid the problem of
multiple karplus solutions. For example, a coupling greater than 8 Hz
is translated to a phi dihedral of -140 +/- 40, even though +140 is also
a valid solution to the karplus equation (granted that +140 is out in
the no-mans land of the Ramachandran plot). Is this sort of thing
considered standard practice? Is it even worth doing on a small system
(15 residues)?
Thanks
Andrew Borgert
John Kuszewski wrote:
> It's hard to say for certain without reading your scripts, but are you
> sure
> that the square well width (in Hz) that you're using with the
> potential is
> less than the tolerance (in Hz) above which you declare a particular
> Jcoup
> restraint to be violated?
>
> Also note that even if your violation tolerance is greater than
> your squarewell width, you can still introduce errors. That's because
> the
> forces created by the Jcoup potential depend on the magnitude of the
> difference between the calculated coupling and the edge of the tolerated
> region, ie., Jobserved +/- squarewell-width. So if your squarewell width
> is 0.5 Hz, and a particular restraint is violated by 0.6 Hz, the
> atomic forces
> are only 3% of what they would be if you'd used the harmonic potential.
> So even if though it's violated, that Jcoup restraint is not pushed
> back into
> place very hard.
>
> Generally speaking, you should keep the Jcoup potential as harmonic.
> Problems in your structure are far more likely to be caused by
> mis-assigned
> NOEs than by 3J couplings.
>
> --JK
>
> On Aug 14, 2007, at 12:23 PM, Andrew Borgert wrote:
>
>> I am running an SA script in vacuum on a small glycopeptide, and I
>> noticed something strange (to me at least) happen when I changed the
>> j-coupling potential type. I initially ran my script using a harmonic
>> potential for the backbone j-coupling ( C-N-CA-C ), however when I
>> switched to a square potential, the number of j-coupling restraint
>> violations over the ensemble of structures increased dramatically (by a
>> factor of about 2) while the number of violations of other types of
>> restraints (noe, dihedral, bond, angle etc.) stayed the same. This
>> seems somewhat counter-intuitive, as switching to a square potential
>> should be akin to 'loosening' the restraints a bit, which should result
>> in fewer violations. Any thoughts?
>> I realize that my description of the problem is rather vague, so I'm not
>> looking for specific trouble shooting, just general advice.
>> I am running xplor_nih 2.12.
>>
>> Thanks
>> Andrew Borgert
>> Biophysical Sciences and Medical Physics
>> University of Minnesota
>>
>> _______________________________________________
>> Xplor-nih mailing list
>> Xplor-nih at nmr.cit.nih.gov
>> http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
