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

[K.A. Feenstra]

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!


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
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