Force field dependence of NMR-based restrained molecular dynamics DNA structure calculations including an analysis of the influence of residual dipolar coupling restraints
- Washington State University Tri-Cities
Restrained molecular dynamics is widely used to calculate DNA structures from NMR data. In silico experiments were performed to show that the force field can be significant compared to the NMR restraints in driving the final structures to converge. A canonical B-DNA model was used as a target structure. Distances, dihedral angles and simulated residual dipolar couplings were calculated from the target structure and used as restraints. X-PLOR and Discover, which use the CHARMM and AMBER force fields, respectively, produced different final structures despite the use of identical distance and dihedral restraints. Incorporation of residual dipolar coupling restraints in X-PLOR improved convergence to the known target structure indicating that the force field dependence can potentially be overcome if residual dipolar coupling restraints are employed.
- Research Organization:
- Washington State University
- Sponsoring Organization:
- USDOE Office of Science (SC)
- DOE Contract Number:
- FG03-02ER63350
- OSTI ID:
- 840902
- Report Number(s):
- DOE/ER/63350-3
- Journal Information:
- Journal of Biomolecular Structure and Dynamics, Journal Name: Journal of Biomolecular Structure and Dynamics Journal Issue: 4 Vol. 20
- Country of Publication:
- United States
- Language:
- English
Similar Records
Determination of the conformation of d(GGAAATTTCC) sub 2 in solution by use of sup 1 H NMR and restrained molecular dynamics
Solution structure of phage. lambda. half-operator DNA by use of NMR, restrained molecular dynamics, and NOE-based refinement