Simulation report
Technical information
General information
Name: Active-like fzd6 sag1.3-bound
PDB id: HOMO
Submitted by: Schulte lab, Karolinska Institutet
System setup
Solvent type: TIP3P
Membrane type: Homogeneous
Membrane composition: POPC
Ionic composition: Chloride (168 mM), Sodium ion (151 mM)
Number of molecules:
Water: 31336
POPC: 300
Chloride: 95
Sodium ion: 85
Protonated smoothened agonist: 1
Frizzled-6: 1
Total number of atoms: 140198
Simulation details
Software and version: GROMACS, 2016.5
Forcefield and version: CHARMM, 36m
Time step : 2.0 fs
Delta : 0.2 ns
Replicates: 3
Accumulated simulation time: 3.0006000000000004 µs
Additonal parameters: Available at "Simulation protocol & starting files"
References
Kozielewicz P, Turku A, Bowin C-F, Petersen J, Valnohova J, Consuelo Alonso Cañizal M, Ono Y, Inoue A, Hoffmann C, Schulte G. 2020. Structural insight into small molecule action on Frizzleds. Nature communications 1 (11). doi: 10.1038/s41467-019-14149-3. (https://doi.org/10.1038/s41467-019-14149-3)
GPCRmd publication page: 1466
