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Simulation report

Technical information

General information

Name: Beta-1 adrenergic receptor in complex with jblumbnibnhrso-jtqlqieisa-n

PDB id: 2YCZ

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 (160 mM), Chloride (207 mM)

Number of molecules:

Water: 20172

POPC: 195

Chloride: 75

Sodium ion: 58

4-{[(2s)-3-(tert-butylamino)-2-hydroxypropyl]oxy}-3-iodo-1h-indole-2-carbonitrile: 1

Beta-1 adrenergic receptor: 1

Total number of atoms: 92017

Simulation details

Software and version: ACEMD3, GPUGRID

Forcefield and version: CHARMM, c36 Jul 2020

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"

Simulation components

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



Water

Specific State ID: 5151

(20172 molecules)

H2O


POPC

Specific State ID: 5152

(195 molecules)


Sodium ion

Specific State ID: 5153

(58 molecules)

Na+


Chloride

Specific State ID: 5154

(75 molecules)

Cl-


4-{[(2s)-3-(tert-butylamino)-2-hydroxypropyl]oxy}-3-iodo-1h-indole-2-carbonitrile (orthosteric lig.)

Specific State ID: 5244

(1 molecule)


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