Simulation report
Technical information
General information
Name: Partially thermostabilized beta-1 adrenergic receptor in complex with (r)-dobutamine
PDB id: 2Y00.B
Activation state: Inactive
Description: Classical unbiased (NVT ensemble) complex flexibility assay.
Submitted by: GPCRmd community
System setup
Solvent type: TIP3P
Membrane type: Homogeneous
Membrane composition: POPC
Ionic composition: Sodium ion (159 mM), Chloride (208 mM)
Number of molecules:
Water: 16040
POPC: 177
Chloride: 60
Sodium ion: 46
(R)-DOBUTAMINE: 1
Beta-1 adrenergic receptor: 1
Total number of atoms: 76842
Simulation details
Software and version: ACEMD, GPUGRID
Forcefield and version: CHARMM, 36m Feb 2016
Time step : 4.0 fs
Delta : 0.2 ns
Replicates: 3
Accumulated simulation time: 1.5 µs
Additonal parameters: Available at "Simulation protocol & starting files"
References
Ismael Rodríguez-Espigares, Mariona Torrens-Fontanals, et al.. 2020. GPCRmd uncovers the dynamics of the 3D-GPCRome. Nature methods 17 (8). doi: 10.1038/s41592-020-0884-y. (http://doi.org/10.1038/s41592-020-0884-y)
Simulation components
Ligands
Receptor
Mutations
Table of simulated mutations
(Mutations shown in blue at the viewer)
| Residue ID | Residue seq. position | Generic num. | From | To |
|---|---|---|---|---|
| 227 | 227 | 5x58 | Y | A |
| 282 | 282 | 6x27 | A | L |
Other molecules
