× Due to a recent server update, this page will be slow for the next 1-2 hours. We apologize for any inconvenience this may cause.

Simulation report

Technical information

General information

Name: Thromboxane a2 receptor in complex with daltroban

PDB id: 6IIV

Activation state: Inactive

Description: Classical unbiased (NVT ensemble) complex flexibility assay.

Submitted by: Francho Nerín-Fonz, IMIM

System setup

Solvent type: Implicit

Membrane type: Homogeneous

Membrane composition: CLR (0.4%), POPC (99.6%)

Ionic composition: Sodium ion (161 mM), Chloride (196 mM)

Number of molecules:

Water: 17274

POPC: 227

Chloride: 61

Sodium ion: 50

Daltroban: 1

Cholesterol: 1

Thromboxane A2 receptor: 1

Total number of atoms: 87588

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

Ligands

Orthosteric ligand(s)

Daltroban

(1 molecule)


Receptor

Visualization and trajectory sharing powered by NGL viewer and MDSrv

Open with GPCRmd Workbench

Mutations

No mutations found



Other molecules



POPC

Specific State ID: 5152

(227 molecules)


Daltroban (orthosteric lig.)

Specific State ID: 5248

(1 molecule)


Chloride

Specific State ID: 5154

(61 molecules)

Cl-


Sodium ion

Specific State ID: 5153

(50 molecules)

Na+


Cholesterol

Specific State ID: 5166

(1 molecule)


Water

Specific State ID: 5151

(17274 molecules)

H2O