Simulation report

Technical information

General information

Name: C-x-c chemokine receptor type 4 in complex with vmip-ii w5c mutant.

PDB id: 4RWS

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 (159 mM), Chloride (202 mM)

Number of molecules:

Water: 22292

POPC: 187

Chloride: 81

Sodium ion: 64

C-X-C chemokine receptor type 4: 1

Viral macrophage inflammatory protein 2: 1

Total number of atoms: 98073

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

Peptidic ligand(s)

Viral macrophage inflammatory protein 2

(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)

Viral macrophage inflammatory protein 2

Residue Generic num. From To
28 - W C


Other molecules



Sodium ion

Specific State ID: 5016

(64 molecules)

Na+


Chloride

Specific State ID: 5017

(81 molecules)

Cl-


POPC

Specific State ID: 5018

(187 molecules)


Water

Specific State ID: 5019

(22292 molecules)

H2O