Influence of non-bonded parameters on the quality of NMR structures: a new force field for NMR structure calculation.
The effects of different non-bonded parameters of force fields for NMR structure calculation on the quality of the resulting NMR solution structures were investigated using Interleukin 4 as a model system. NMR structure ensembles were calculated with an ab initio protocol using torsion angle dynamics. The calculations were repeated with five different non-bonded energy functions and parameters. The resulting ensembles were compared with the available X-ray structures, and their quality was assessed with common structure validation programs. In addition, the impact of torsion angle restraints and dihedral energy terms for the sidechains and the backbone was studied. The further improvement of the quality by refinement in explicit solvent was demonstrated. The optimal parameters, including those necessary for water refinement, are available in the new version of the PARALLHDG force field.
Linge
J P
JP
European Molecular Biology Laboratory, Meyerhofstrassee 1, D-69012 Heidelberg, Germany.
Nilges
M
M
D015847:Interleukin-4 / Q000737:chemistry; D008432:Mathematical Computing; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*
D015847:Interleukin-4