Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, andKollm
structuresolution
Amber
10
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, andKollm
refinement
CORMA
T.L. James
structurevalidation
Refinement
Method: simulated annealing / Software ordinal: 1 Details: The upper bounds obtained from MARDIGRAS were multiplied by a factor 1.25 before being exported to Amber 10 for a 25 ps simulated annealing protocol. The simulated annealing protocol using ...Details: The upper bounds obtained from MARDIGRAS were multiplied by a factor 1.25 before being exported to Amber 10 for a 25 ps simulated annealing protocol. The simulated annealing protocol using the pairwise generalized Born model was as follows: the temperature of the system was kept constant at 600 K during the first 5 ps, cooled down slowly to 100 K between 5-18 ps, and cooled down to 0 K for the last 7 ps. The protocol was repeated 50 times to obtain an NMR ensemble with the 10 lowest RMSD structures. The structure with the lowest RMSD of the ensemble was put back into MARDIGRAS for a second and third cycle of NOE calibration and structure calculations.
NMR representative
Selection criteria: closest to the average
NMR ensemble
Conformer selection criteria: lowest RMSD to average structure Conformers calculated total number: 50 / Conformers submitted total number: 10
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