A dynamic pentameric ligand-gated ion channel resting state by cryo-electron microscopy
Year: 2020
Type: article
Abstract: 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.
Authors: Rovšnik, Urška, Zhuang, Yuxuan, Axelsson, Linnea, Forsberg, Björn, Lim, Victoria, Carroni, Marta, Blau, Christian, Howard, Rebecca, Lindahl, Erik
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W6893658207