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. Author manuscript; available in PMC: 2015 Jun 1.
Published in final edited form as: J Magn Reson. 2014 Apr 2;243:54–64. doi: 10.1016/j.jmr.2014.03.011

Table 2.

Energy functions, topology and parameters of the four different force fields used in the structure calculations.a

Model ENONB b topology/parameters nonbonded parameters
REPEL EVDW-REPEL protein.top/protein.par krep >0, Crep >0
VDW EVDW proteinEEFx.top/proteinEEFx.par krep=0, group, vswitch, ctonnb=7 Å, ctofnb=9Å
vacuum EVDW + EELEC proteinEEFx.top/proteinEEFx.par krep=0, group, vswitch, ctonnb=7Å, ctofnb=9Å, switch, rdie
EEFx Evdw + EELEC + Eslv proteinEEFx.top/proteinEEFx.par krep=0, group, vswitch, ctonnb=7Å, ctofnb=9Å, switch, rdie, ron=7Å, roff=9Å
a

All calculations were performed with nbxmod=5, or nbxmod=3 for REPEL, to allow repulsions only between atoms separated by more than two covalent bonds. Calculations using the torsionDB potential were performed with nbxmod=4 to allow repulsions only between atoms separated by more than three covalent bonds.

b

ENONB is the XPLOR-NIH nonbonded energy function where EVDW-EWPWL is the simple repulsive form of the XPLOR van der Waals function, EVDW is the switched Lennard-Jones form of the XPLOR van der Waals function and EELEC is the switched distance-dependent dielectric form of the XPLOR electrostatic function [29]. Eslv and its switching function with parameters ron and roff are described in equations 3–4.