[Xplor-nih] Problems constraining a guanine residue to syn conformation

[John Kuszewski]

Hi,

Step one:  Try it again with the nucleic.top/nucleic.par files, since  
those are the current ones
(and based on parallhdg.dna, so they're not too different).

Step two:  Take a look at your script.  Are you sure you have the NOE  
term on?  Is the force constant
reasonable?


On Feb 20, 2007, at 1:48 PM, yu269821 at yorku.ca wrote:

> Hello,
>
> I am calculating RNA structures using the 2.16.0 version of XPLOR-NIH.
> I am using parallhdg.dna as my parameter file. I am having trouble
> constraining a guanine residue to a syn conformation. Normally one
> intranuclear restraint (H8 to H1' constrained to 2.15 0.35 0.65)  
> should
> be sufficient, however this restraint keeps being violated even if
> that is the only restraint used for that residue (I also have no  
> hydrogen
> bonding, dihedral angles planarity restraints for that residue) in
> about half of my structures. Can this be a problem with my parameter
> file may be something else?
>
> Thank you in advance,
> Alex Beribisky.
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