Simulation report

Technical information

General information

Name: Proteinase-activated receptor 1 in complex with vorapaxar

PDB id: 3VW7.A

Activation state: Intermediate

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 (161 mM), Chloride (182 mM)

Number of molecules:

Water: 13104

POPC: 154

Chloride: 43

Sodium ion: 38

Vorapaxar: 1

Proteinase-activated receptor 1: 1

Total number of atoms: 64843

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)

Vorapaxar

(1 molecule)


Receptor

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Mutations

No mutations found



Other molecules



Sodium ion

Specific State ID: 5016

(38 molecules)

Na+


Chloride

Specific State ID: 5017

(43 molecules)

Cl-


POPC

Specific State ID: 5018

(154 molecules)


Water

Specific State ID: 5019

(13104 molecules)

H2O


Vorapaxar (orthosteric lig.)

Specific State ID: 5094

(1 molecule)