Atomistic molecular dynamics trajectories of the glutamine-binding protein GlnBP

The directory “glnbp-complex” contains 5 simulation trajectories in Amber format starting from the ligand-bound crystal structure of GlnBP with PDB identifier 1WDN. 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.

The simulation frames of all trajectory files were extracted at invervals of 1 nanoseconds. Water was removed to reduce files sizes. The simulations were performed with the AMBER20 software and the ff14SB force field parameters in explicit TIP3P water. The two simulation systems with and without ligand were carefully relaxed in 9 steps according to the AMBER tutorial “Relaxation of explicit water systems” (see https://ambermd.org/tutorials/).