Simulation report
Technical information
General information
Name: Uman smoothened receptor (apoform)
PDB id: 6OT0
Activation state: Active
Submitted by: Schulte lab, Karolinska Institutet
System setup
Solvent type: TIP3P
Membrane type: Homogeneous
Membrane composition: POPC
Ionic composition: Chloride (572 mM), Sodium ion (550 mM)
Number of molecules:
Water: 10000
POPC: 301
Chloride: 103
Sodium ion: 99
Smothened agonist: 1
Smoothened homolog: 1
Total number of atoms: 156399
Simulation details
Software and version: GROMACS, 2019.2
Forcefield and version: CHARMM36, GAFF2, CHARMM36, GAFF2
Time step : 2.0 fs
Delta : 0.3 ns
Replicates: 4
Accumulated simulation time: 1.2507000000000001 µs
Additonal parameters: Available at "Simulation protocol & starting files"
References
Ainoleena Turku; Hannes Schihada; Pawel Kozielewicz; Carl-Fredrik Bowin; Gunnar Schulte. 2021. Residue 6.43 defines receptor function in class F GPCRs. Nature communications 12 (1). doi: 10.1038/s41467-021-24004-z. (https://doi.org/10.1038/s41467-021-24004-z)
GPCRmd publication page: 1473
Simulation components
Receptor
Mutations
Table of simulated mutations
| Residue ID | Residue seq. position | Generic num. | From | To |
|---|
