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Simulation report

Technical information

General information

Name: 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: Chloride (204 mM), Sodium ion (160 mM)

Number of molecules:

Water: 18794

POPC: 184

Chloride: 69

Sodium ion: 54

(R)-DOBUTAMINE: 1

Beta-1 adrenergic receptor: 1

Total number of atoms: 86234

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)



GPCRmd publication page: 1469

Simulation components

Ligands

Orthosteric ligand(s)

(r)-dobutamine

(1 molecule)


Receptor

Visualization and trajectory sharing powered by NGL viewer and MDSrv

Open with GPCRmd Workbench

Mutations

Table of simulated mutations

Residue ID Residue seq. position Generic num. From To


Other molecules



(R)-DOBUTAMINE (orthosteric lig.)

Specific State ID: 5029

(1 molecule)


Chloride

Specific State ID: 5017

(69 molecules)

Cl-


POPC

Specific State ID: 5018

(184 molecules)


Water

Specific State ID: 5019

(18794 molecules)

H2O


Sodium ion

Specific State ID: 5016

(54 molecules)

Na+


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