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

[K.A. Feenstra]

Chris Spronk wrote:
> 
> Hi there,
> 
> 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....

In my opinion, being neither an NMR expert nor familiar with all the
details of the implementation in Gromacs, there would be two possible
cases for which one could use a dihedral restraint. I might be 
overlooking some important desired feature, or restrictions in the 
current implementation, so feel free to correct or supplement me 
when and where necessary! 

One of the situations would be to
keep the dihedral fixed. In that case it is probably always possible
to define it far from 180 degrees, and additionally one should put
the potential steep enough to preclude 'flipping' (which is the whole
point if you want to keep it fixed). 

The other situation would be to
restrain the dihedral to one of a number of minima (e.g. only staggered
or only eclypsed). In that case, one should take a proper dihedral
with the appropriate multiplicity. Here, the hight of the barriers
is not restricted, and could be so high that flips are rare or even
impossible, or so low that they will be effortless.

Both cases seem to me to be perfectly possible in the current 
implementation. 

As for something more like the distance restraints,
I am not sure what you mean by that. Is it the form of the potential
(i.e. with an optional flat part in between the harmonics and a
linear part beyond a certain point) or is it the possibilities of
doing averaging over a group of (ambiguous) distances/angles and/or
time and ensemble averages? 
As for the form of the potential I don't see the distance restraints
potential as being applicable to dihedral angles. For all sorts of
averagings, I don't know whether these are experimentally relevant
for dihedrals, but I can imagine they could be.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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