Simulation report

Technical information

General information

Name: C-x-c chemokine receptor type 4 in complex with 1t

PDB id: 3ODU.A

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 (162 mM)

Number of molecules:

Water: 13408

POPC: 173

Chloride: 50

Sodium ion: 39

It1t: 1

C-X-C chemokine receptor type 4: 1

Total number of atoms: 68317

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)

It1t

(1 molecule)


Receptor

Visualization and trajectory sharing powered by NGL viewer and MDSrv

Open with GPCRmd Workbench

Mutations

No mutations found



Other molecules



Sodium ion

Specific State ID: 5016

(39 molecules)

Na+


Chloride

Specific State ID: 5017

(50 molecules)

Cl-


POPC

Specific State ID: 5018

(173 molecules)


It1t (orthosteric lig.)

Specific State ID: 5067

(1 molecule)


Water

Specific State ID: 5019

(13408 molecules)

H2O