Simulation report

Technical information

General information

Name: Active conformation of gpcr opsin stabilized by octylglucoside (apoform)

PDB id: 4J4Q

Activation state: Active

Description: Simulations generated using Adaptive sampling protocol. Each of the replicates corresponds to one stage of the simulation.

Submitted by: George Khelashvili, Weill Cornell Medical College

System setup

Solvent type: TIP3P

Membrane type: Heterogeneous

Membrane composition: POPG (9.1%), POPC (90.9%)

Ionic composition: Sodium ion (144 mM), Chloride (80 mM)

Number of molecules:

Water: 27006

POPC: 300

Sodium ion: 70

Chloride: 39

ZINC8437540: 30

Rhodopsin: 1

Total number of atoms: 130395

Simulation details

Software and version: ACEMD,

Forcefield and version: CHARMM, 36m Jul 2017

Time step : 2.0 fs

Delta : 1.6 ns

Replicates: 4

Accumulated simulation time: 51.608 µs

Additonal parameters: Available at "Simulation protocol & starting files"



References

Giulia Morra, Asghar M Razavi, Kalpana Pandey, Harel Weinstein, Anant K Menon, George Khelashvili. 2018. Mechanisms of Lipid Scrambling by the G Protein-Coupled Receptor Opsin. Structure 26 (2). doi: 10.1016/j.str.2017.11.020. (https://doi.org/10.1016/j.str.2017.11.020)


Simulation components

Receptor

PDB id: 4J4Q
Rhodopsin

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Mutations

No mutations found



Other molecules



Sodium ion

Specific State ID: 5016

(70 molecules)

Na+


Chloride

Specific State ID: 5017

(39 molecules)

Cl-


POPC

Specific State ID: 5018

(300 molecules)


Water

Specific State ID: 5019

(27006 molecules)

H2O


ZINC8437540

Specific State ID: 5123

(30 molecules)