Simulation report
Technical information
General information
Name: Dopamine d2 receptor (apoform) (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: SDPC (3.9%), CHL1 (32.8%), SM18 (24.5%), DOPC (7.5%), DSPC (9.3%), DPPC (22.1%)
Number of molecules:
Cholesterol: 110
N-palmitoylsphingomyelin: 82
1,2-dipalmitoylphosphatidylcholine: 74
DSPC: 31
DOPC: 25
1-stearoyl-2-docosahexanoyl-sn-glycero-3-phosphocholine: 13
D(2) dopamine receptor: 1
Total number of atoms: 42802
Simulation details
Software and version: ACEMD, 3.3.0
Forcefield and version: CHARMM, CHARMM36m
Time step : 4.0 fs
Delta : 0.8 ns
Replicates: 4
Accumulated simulation time: 3.6056000000000004 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
(Mutations shown in blue at the viewer)
| Residue ID | Residue seq. position | Generic num. | From | To |
|---|---|---|---|---|
| 400 | 219 | 5x68 | R | - |
| 400 | 219 | 5x68 | K | - |
| 400 | 219 | 5x68 | R | - |
| 400 | 219 | 5x68 | V | - |
| 400 | 219 | 5x68 | N | - |
| 400 | 219 | 5x68 | T | - |
| 400 | 219 | 5x68 | K | - |
| 400 | 219 | 5x68 | R | - |
| 400 | 219 | 5x68 | S | - |
| 400 | 219 | 5x68 | S | - |
| 400 | 219 | 5x68 | R | - |
| 400 | 219 | 5x68 | A | - |
| 400 | 219 | 5x68 | F | - |
| 400 | 219 | 5x68 | R | - |
| 400 | 219 | 5x68 | A | - |
| 400 | 219 | 5x68 | H | - |
| 400 | 219 | 5x68 | L | - |
| 400 | 219 | 5x68 | R | - |
| 400 | 219 | 5x68 | A | - |
| 400 | 219 | 5x68 | P | - |
| 400 | 219 | 5x68 | L | - |
| 400 | 219 | 5x68 | K | - |
| 400 | 219 | 5x68 | G | - |
| 400 | 219 | 5x68 | N | - |
| 400 | 219 | 5x68 | C | - |
| 400 | 219 | 5x68 | T | - |
| 400 | 219 | 5x68 | H | - |
| 400 | 219 | 5x68 | P | - |
| 400 | 219 | 5x68 | E | - |
| 400 | 219 | 5x68 | D | - |
| 400 | 219 | 5x68 | M | - |
| 400 | 219 | 5x68 | K | - |
| 400 | 219 | 5x68 | L | - |
| 400 | 219 | 5x68 | C | - |
| 400 | 219 | 5x68 | T | - |
| 400 | 219 | 5x68 | V | - |
| 400 | 219 | 5x68 | I | - |
| 400 | 219 | 5x68 | M | - |
| 400 | 219 | 5x68 | K | - |
| 400 | 219 | 5x68 | S | - |
| 400 | 219 | 5x68 | N | - |
| 400 | 219 | 5x68 | G | - |
| 400 | 219 | 5x68 | S | - |
| 400 | 219 | 5x68 | F | - |
| 400 | 219 | 5x68 | P | - |
| 400 | 219 | 5x68 | V | - |
| 400 | 219 | 5x68 | N | - |
| 400 | 219 | 5x68 | R | - |
| 400 | 219 | 5x68 | R | - |
| 400 | 219 | 5x68 | R | - |
| 400 | 219 | 5x68 | V | - |
| 400 | 219 | 5x68 | E | - |
| 400 | 219 | 5x68 | A | - |
| 400 | 219 | 5x68 | A | - |
| 400 | 219 | 5x68 | R | - |
| 400 | 219 | 5x68 | R | - |
| 400 | 219 | 5x68 | A | - |
| 400 | 219 | 5x68 | Q | - |
| 400 | 219 | 5x68 | E | - |
| 400 | 219 | 5x68 | L | - |
| 400 | 219 | 5x68 | E | - |
| 400 | 219 | 5x68 | M | - |
| 400 | 219 | 5x68 | E | - |
| 400 | 219 | 5x68 | M | - |
| 400 | 219 | 5x68 | L | - |
| 400 | 219 | 5x68 | S | - |
| 400 | 219 | 5x68 | S | - |
| 400 | 219 | 5x68 | T | - |
| 400 | 219 | 5x68 | S | - |
| 400 | 219 | 5x68 | P | - |
| 400 | 219 | 5x68 | P | - |
| 400 | 219 | 5x68 | E | - |
| 400 | 219 | 5x68 | R | - |
| 400 | 219 | 5x68 | T | - |
| 400 | 219 | 5x68 | R | - |
| 400 | 219 | 5x68 | Y | - |
| 400 | 219 | 5x68 | S | - |
| 400 | 219 | 5x68 | P | - |
| 400 | 219 | 5x68 | I | - |
| 400 | 219 | 5x68 | P | - |
| 400 | 219 | 5x68 | P | - |
| 400 | 219 | 5x68 | S | - |
| 400 | 219 | 5x68 | H | - |
| 400 | 219 | 5x68 | H | - |
| 400 | 219 | 5x68 | Q | - |
| 400 | 219 | 5x68 | L | - |
| 400 | 219 | 5x68 | T | - |
| 400 | 219 | 5x68 | L | - |
| 400 | 219 | 5x68 | P | - |
| 400 | 219 | 5x68 | D | - |
| 400 | 219 | 5x68 | P | - |
| 400 | 219 | 5x68 | S | - |
| 400 | 219 | 5x68 | H | - |
| 400 | 219 | 5x68 | H | - |
| 400 | 219 | 5x68 | G | - |
| 400 | 219 | 5x68 | L | - |
| 400 | 219 | 5x68 | H | - |
| 400 | 219 | 5x68 | S | - |
| 400 | 219 | 5x68 | T | - |
| 400 | 219 | 5x68 | P | - |
| 400 | 219 | 5x68 | D | - |
| 400 | 219 | 5x68 | S | - |
| 400 | 219 | 5x68 | P | - |
| 400 | 219 | 5x68 | A | - |
| 400 | 219 | 5x68 | K | - |
| 400 | 219 | 5x68 | P | - |
| 400 | 219 | 5x68 | E | - |
| 400 | 219 | 5x68 | K | - |
| 400 | 219 | 5x68 | N | - |
| 400 | 219 | 5x68 | G | - |
| 400 | 219 | 5x68 | H | - |
| 400 | 219 | 5x68 | A | - |
| 400 | 219 | 5x68 | K | - |
| 400 | 219 | 5x68 | D | - |
| 400 | 219 | 5x68 | H | - |
| 400 | 219 | 5x68 | P | - |
| 400 | 219 | 5x68 | K | - |
| 400 | 219 | 5x68 | I | - |
| 400 | 219 | 5x68 | A | - |
| 400 | 219 | 5x68 | K | - |
| 400 | 219 | 5x68 | I | - |
| 400 | 219 | 5x68 | F | - |
| 400 | 219 | 5x68 | E | - |
| 400 | 219 | 5x68 | I | - |
| 400 | 219 | 5x68 | Q | - |
| 400 | 219 | 5x68 | T | - |
| 400 | 219 | 5x68 | M | - |
| 400 | 219 | 5x68 | P | - |
| 400 | 219 | 5x68 | N | - |
| 400 | 219 | 5x68 | G | - |
| 400 | 219 | 5x68 | K | - |
| 400 | 219 | 5x68 | T | - |
| 400 | 219 | 5x68 | R | - |
| 400 | 219 | 5x68 | T | - |
| 400 | 219 | 5x68 | S | - |
| 400 | 219 | 5x68 | L | - |
| 400 | 219 | 5x68 | K | - |
| 400 | 219 | 5x68 | T | - |
| 400 | 219 | 5x68 | M | - |
| 400 | 219 | 5x68 | S | - |
| 400 | 219 | 5x68 | R | - |
| 400 | 219 | 5x68 | R | - |
| 400 | 219 | 5x68 | K | - |
| 400 | 219 | 5x68 | L | - |
| 400 | 219 | 5x68 | S | - |
