A dynamic pentameric ligand-gated ion channel resting state by cryo-electron microscopy

Density guided simulations files

.mrc files - CryoEM density half-maps for pH 7, pH 5, pH 3

.mdp - Option files for GROMACS simulations. One density guided mdp file and one annealing mdp file per pH data set

.gro - Equilibrated starting model of manually built pH 7, the same was used for all three pH data sets

.itp - topology files

.top - topology master file

Example command for density guided simulations

gmx grompp --f mdrun_ip_ph3_tc40_sp02_tau0_3.mdp --p topology.top --o mdrun_ip_ph3_tc40_sp02_tau0_3.tpr --c minimized.gro

gmx mdrun --s mdrun_ip_ph3_tc40_sp02_tau0_3_test.tpr --v --x mdrun.xtc --g md.log --e ener.edr --c final_ip_ph3_tc40_sp02_tau0_3_test.gro 

Example command for custom GROMACS FSC tool, available at (https://github.com/blauc/gromacs/tree/fscavg)

gromacs-fsc/bin/gmx fsc -f whole.xtc -s mdrun_ip_ph3_tc40_sp02_tau0_3_test.tpr -refmap pH3_half1_class001_unfil.mrc -dt 100 -xvg none -shells 186 -o fsc_ip_ph3_tc40_sp02_tau0_3.xvg -similarity similarity_ip_ph3_tc40_sp02_tau0_3.xvg -avg fscavg_ip_ph3_tc40_sp02_tau0_3.xvg -fscmove fscmove_ip_ph3_tc40_sp02_tau0_3.xvg -ordinate-axis fscaxis_ip_ph3_tc40_sp02_tau0_3.xvg -fscmoveavg fscmoveavg_ip_ph3_tc40_sp02_tau0_3.xvg

Molecular dynamics simulations

.prep_file - topology files and forcefield files for preparing the simulations.

.run_tpr - tpr files for production runs

.prodution_traj - concatenated trajectories and starting snapshots (after equilibration).

analysis_results
- csv: analaysis data
- ipynb: jupyter notebook for generating the figures in the paper.