Simulation report

Technical information

General information

Name: Partially thermostabilized beta-1 adrenergic receptor in complex with 4-(1-piperazinyl)-1h-indole

PDB id: 3ZPQ.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 (207 mM), Sodium ion (164 mM)

Number of molecules:

Water: 16937

POPC: 189

Chloride: 63

Sodium ion: 50

4-(1-piperazinyl)-1h-indole: 1

Beta-1 adrenergic receptor: 1

Total number of atoms: 81132

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

Orthosteric ligand(s)

4-(1-piperazinyl)-1h-indole

(1 molecule)


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


Other molecules



Sodium ion

Specific State ID: 5016

(50 molecules)

Na+


Chloride

Specific State ID: 5017

(63 molecules)

Cl-


POPC

Specific State ID: 5018

(189 molecules)


Water

Specific State ID: 5019

(16937 molecules)

H2O


4-(1-piperazinyl)-1h-indole (orthosteric lig.)

Specific State ID: 5096

(1 molecule)