Simulations of membrane proteins in a mixture of lipids with varying levels of chain unsaturation

Four structurally distinct membrane proteins were simulated in a mixture of phospholipids. The membranes contained one copy of one of the protein types with equimolar concentrations of DPPC, DOPC, DLiPC, SDPC, and cholesterol. The CHARMM36 force field [1] was employed, and the systems were built using the CHARMM-GUI web portal [2]. The 4-microsecond long simulations were performed using GROMACS [3]. Further details on the setup of the systems as well as on the simulation protocol can be found in the related paper at DOI: 10.1371/journal.pcbi.1007033.

The files are named based on the PDB codes of the proteins (1AFO, 2M0B, 3EML, and 3EMN). For each system, the original simulation run input file (tpr) and the corresponding outputs (xtc, edr) are provided. Additionally, the simulations can be extended using the continue point (cpt) file. For each system the files required to generate the run input file are also provided: the topology file (top), index file (ndx), and a common run parameter file (mdp). The CHARMM36 force field can be downloaded from http://mackerell.umaryland.edu/charmm_ff.shtml

Notably, the protein definition files (itp) were re-generated. After performing these simulations, the atom ordering of cholesterol in the CHARMM36 force field was changed. The provided gro files, as well as the lipid definition files (itp) correspond to this new atom order. While they can be used to generate a run input file, yet this run input file will not be identical to the one provided. Therefore: 1) for analysis, the provided xtc+tpr files are fine; 2) for extending the simulation, the tpr+cpt files are fine; 3) for new simulations, the tpr file can be generated based on the provided files, yet it cannot be used together with the provided xtc file.

[1] DOI: 10.1021/jp101759q

[2] DOI: 10.1021/acs.jctc.5b00935

[3] DOI: 10.1016/j.softx.2015.06.001