[gmx-users] Dihedral angle restraints in NMR refinement...

Chris Spronk C.Spronk at cmbi.kun.nl
Wed Sep 25 15:53:12 CEST 2002

Hi there,

I have been playing a little bit with the NMR derived dihedral angle
restraints as defined as impropers. I ran into the following problem: 
Dihedral angle restraints close to 180 degrees give rise to local
heating and a lot of LINCS warnings (and exploding system).

On page 59 of the gromacs manual it is stated that impropers should be
defined as far away from 180 degrees as possible. The reason (dank je
Bert!) is that the periodicity is absent and small changes in the
dihedral angle leading to flips from ~-180 to ~+180 lead to huge
differences in improper dihedral energy.
So when I converted a couple of the dihedrals that were close to 180 ( N
CA CB CG ) to dihedrals around ~60 degrees ( C CA CB CG ) these
restraints did not give rise to any LINCS warnings or heating anymore
(but a little later some others around 170 degrees did).
Although this is a possible work-around it still makes the use of
improper dihedral angles for dihedral angle restraints rather 
impractical. In addition, I think it limits the sampling of conformations.

So I was hoping someone of the developers-team could help us (the NMR
users) with this. In addition it would still be nice to have a restraint
type similar to the distance restraints, with zero force between an
upper and lower bound for the angle to account for the experimental 
uncertainty, and a harmonic potential outside
these bounds. I hope this is not too big of a problem, but otherwise NMR
people will probably not be prompted to use GROMACS and I personally
think that would be a great pity....

thanks in advance,


PS For those who may be interested: I have written a python script that
converts XPLOR distance and dihedral restraints to GROMACS format. Mail 
me for the details.....

K.A. Feenstra wrote:

 > Patrick Ladam wrote:
 >>Thank you for the script. Concerning dihedral
 >>angles, last time I asked the question, I was
 >>answered to turn dihedral angles into distances
 >>restraints, which is not correct. Concerning
 >>using impropers for dihedral restraints, this is
 >>not suitable for our needs, an improper concerns
 >>an atom types and we do not want all the atoms
 >>of these types to be at a certain value. Or maybe
 >>is there a way to use atom numbers from the pdb
 >>file like for dist restraints?
 > For some of the forcefields in Gromacs, interaction *types* are
 > defined based on combinations of atom types. But, all molecules
 > will be written as an explicit topology somewhere in your .top
 > file. There all interactions (bonds, angles, dihedrals etc) are
 > defined explicitly, although the parameters might be omitted
 > which will lead to using the implicit 'type' parameters.
 > But, you can also *explicitly* set your parameters in the .top
 > file. There you are! Add a line to the impropers section for
 > the improper dihedral you are adding, and specify the force
 > constant on that line too!

Chris Spronk
Centre for Molecular and Biomolecular Informatics
University of Nijmegen
Toernooiveld 1
NL-6500 GL Nijmegen
The Netherlands
fax  :	+31/+24/3652977
e-mail: C.Spronk at cmbi.kun.nl

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