Molecular dynamics simulation data for the publication "Trapping of spermine, Kukoamine A, and polyamine toxin blockers in GluK2 kainate receptor channels"

This dataset contains unbiased molecular dynamics simulation trajectories, stripped of water and lipid coordinates due to size constraints. It also contains the full initial coordinates for production runs as well as the representative structures for all trajectories.

Description of the data and file structure

The data are deposited as a .zip file and organized into 4 folders, each containing MD simulation data for GluK2SPM, GluK2KukoA, GluK2NpTx8, and GluK2PhTx74 systems.

All trajectory (.nc) files are stripped of water and lipid molecules, and saved sparsely, skipping by 20 frames. Please see the table below for the systems and corresponding topology and trajectory files.

System

# of Frames

Production Length

Topology File

Trajectory File

GluK2SPM

3992

800 ns

GLUK2_SPM_closed_nowat_nolip.prmtop

GLUK2_SPM_closed_traj_nowat_nolip_skip20.nc

GluK2KukoA

2800

560 ns

GLUK2_KUK_closed_nowat_nolip.prmtop

GLUK2_KUK_closed_traj_nowat_nolip_skip20.nc

GluK2PhTx74

2800

560 ns

GLUK2_PTX_closed_nowat_nolip.prmtop

GLUK2_PTX_closed_traj_nowat_nolip_skip20.nc

GluK2NpTx8

2800

560 ns

GLUK2_NTX_closed_nowat_nolip.prmtop

GLUK2_NTX_closed_traj_nowat_nolip_skip20.nc

The full (with waters and lipids) initial structures and representative structures of the trajectories and corresponding topology files are located under each system folder. The topology filenames are in the form of *full.prmtop and the coordinate filenames are in the form of *initial.rst7 and *repres.rst7. Representative structures match the structures shown in Figure 6 in the paper.

MD trajectories in binary NetCDF (.nc) format and the coordinates in .rst7 format can be visualized using VMD after uploading the corresponding topology file (.prmtop).Analysis of the trajectories can be performed using the CPPTRAJ module of AmberTools and VMD.