Atomistic molecular dynamics trajectories of the glutamine-binding protein GlnBP

To enable the unbinding events of the trajectories, all interactions between the protein and the ligand were reduced by 16% by rescaling the partial charges and Lennard-Jones epsilon parameters of the ligand atoms with the commands change charge and changeLJSingleType of the Amber program parmed.

The trajectories have a length of 2 microseconds. The directory “glnbp” contains 20 simulation trajectories in Amber format starting from the ligand-bound crystal structure 1WDN with ligand removed. On 11 of the 20 trajectories with a length up to 4 microseconds, GlnBP changes its conformation from the initial closed conformation of the crystal structure to an open conformation.