Simulation report

Technical information

General information

Name: Partially thermostabilized beta-1 adrenergic receptor (apoform)

PDB id: 4BVN.A

Activation state: Inactive

Description: Classical unbiased (NVT ensemble) sodium allosteric binding assay.

Submitted by: GPCRmd community

System setup

Solvent type: TIP3P

Membrane type: Homogeneous

Membrane composition: POPC

Ionic composition: Chloride (203 mM), Sodium ion (161 mM)

Number of molecules:

Water: 15837

POPC: 169

Chloride: 58

Sodium ion: 46

Beta-1 adrenergic receptor: 1

Total number of atoms: 75112

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

Receptor

Visualization and trajectory sharing powered by NGL viewer and MDSrv

Open with GPCRmd Workbench

Mutations

Table of simulated mutations

(Mutations shown in blue at the viewer)

Residue Generic num. From To
227 5x58 Y A
282 6x27 A L


Other molecules



Sodium ion

Specific State ID: 5016

(46 molecules)

Na+


Chloride

Specific State ID: 5017

(58 molecules)

Cl-


POPC

Specific State ID: 5018

(169 molecules)


Water

Specific State ID: 5019

(15837 molecules)

H2O