Simulation report
Technical information
General information
Name: Dopamine d2 receptor (apoform)
PDB id: 6CM4
Activation state: Inactive
Description: Production simulations for each replica were run for 1 µs each, at constant volume (NVT ensemble), 1013 bar and 310 K
Submitted by: Ramon Guixà-González, Paul Scherrer Institut
System setup
Solvent type: Implicit
Membrane type: Heterogeneous
Membrane composition: DPPC (14.2%), CHL1 (33.1%), DOPC (10.7%), OMEG (13.0%), DSPC (5.3%), PSM (23.7%)
Number of molecules:
Cholesterol: 112
N-palmitoylsphingomyelin: 80
1,2-dipalmitoylphosphatidylcholine: 48
1-stearoyl-2-docosapentaenoyl-3-stearyl-glycerol: 44
DOPC: 36
DSPC: 18
D(2) dopamine receptor: 1
Total number of atoms: 43025
Simulation details
Software and version: ACEMD, 3.3.0
Forcefield and version: CHARMM, CHARMM36m
Time step : 4.0 fs
Delta : 0.3334 ns
Replicates: 4
Accumulated simulation time: 4.0008 µs
Additonal parameters: Available at "Simulation protocol & starting files"
References
Marie-Lise Jobin, Véronique De Smedt-Peyrusse, Fabien Ducrocq, Rim Baccouch, Asma Oummadi, Maria Hauge Pedersen, Brian Medel-Lacruz, Maria-Florencia Angelo, Sandrine Villette, Pierre Van Delft, Laetitia Fouillen, Sébastien Mongrand, Jana Selent, Tarson Tolentino-Cortez, Gabriel Barreda-Gómez, Stéphane Grégoire, Elodie Masson, Thierry Durroux, Jonathan A. Javitch, Ramon Guixà-González, Isabel D. Alves, Pierre Trifilieff. 2023. Impact of membrane lipid polyunsaturation on dopamine D2 receptor ligand binding and signaling. Molecular Psychiatry. doi: 10.1038/s41380-022-01928-6.
GPCRmd publication page: 1495
Simulation components
Receptor
Mutations
Table of simulated mutations
| Residue ID | Residue seq. position | Generic num. | From | To |
|---|
