Role of lipid nanodomains for inhibitory FcγRIIb function

Dataset repository - Role of lipid nanodomains for inhibitory FcγRIIb function === The repository contains setup files and parameter files for atomistic molecular dynamics (MD) simulations performed with the GROMACS 2021/2022 series. Modified trajectories for the post-processing analysis are further included. The repositiory corresponds to the following manuscript: Franziska Spiegel, Marius F.W. Trollmann, Sibel Kara, Matthias Pöhnl, Astrid F. Brandner, Falk Nimmerjahn, Anja Lux, Rainer A. Böckmann bioRxiv 2023.05.09.540011; doi: https://doi.org/10.1101/2023.05.09.540011 Corresponding authors: * Rainer A. Böckmann (rainer.boeckmann@fau.de) * Anja Lux (anja.lux@fau.de) ### XTC/TPRs Directories contain: * md.tpr: GROMACS run file for the whole system * md_nonsolvent.tpr: GROMACS run file for the non-solvent selection (Membrane-Protein only) * md_mol_center_dt10ns.xtc: GROMACS trajectories used during post-processing with a slightly larger spacing (10ns instead of 1ns). * topol.top: GROMACS topology file used for simulations * index.ndx: GROMACS index file used for simulations * toppar: Contains CHARMM36 forcefield parameters for lipids, protein and glycans in GROMACS readable format (.itp) * step6.6_equilibration.gro: Input structure of the last equilibration step (see step6.6_equilibration.mdp) that was used as inital structure for the production simulation * last_frame.gro: Output structure of the production simulation The preparation of the raw trajectories for post-processing was done with GROMACS using the commands: >> gmx trjconv -f md.xtc -s md.tpr -pbc mol -center -n md_traj.ndx -dt 1000 -o md_mol_center.xtc >> gmx trjconv -f md_mol_center.xtc -s md_nonsolvent.tpr -o md_mol_center_dt10ns.xtc -dt 10000 The group for centering was the transmembrane domain of the Fcg receptor, as output only the protein and the membrane was chosen. ### Wild type simulations (No Glycans) * wt_replica_0 * wt_replica_1 * wt_replica_2 * wt_replica_3 * wt_replica_4 * wt_replica_5 * wt_replica_6 * wt_replica_7 * wt_replica_8 ### Mutant simulations (No Glycans) * mut_replica_0 * mut_replica_1 * mut_replica_2 ### Wild type simulations (Glycans) * wt_glycan_replica_0 * wt_glycan_replica_1 * wt_glycan_replica_2 * wt_glycan_replica_3 ### Parameters Simulation parameter files (.mdp) are given for each equilibration step and the final production simulation. Initial input files are obtained from the CHARMM-GUI webserver. * simulation_parameters * mut_wt_no_glycans * wt_glycans ### Co