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Simulation report

Technical information

General information

Name: Smoothened homolog/soluble cytochrome b562 chimeric protein in complex with cyclopamine

PDB id: 4O9R

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 (156 mM), Chloride (163 mM)

Number of molecules:

Water: 25943

POPC: 226

Chloride: 76

Sodium ion: 73

11-deoxojervine: 1

Smoothened homolog: 1

Total number of atoms: 114138

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)

11-deoxojervine

(1 molecule)


Receptor

PDB id: 4O9R
Smoothened homolog

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Open with GPCRmd Workbench

Mutations

No mutations found



Other molecules



POPC

Specific State ID: 5152

(226 molecules)


11-deoxojervine (orthosteric lig.)

Specific State ID: 5241

(1 molecule)


Chloride

Specific State ID: 5154

(76 molecules)

Cl-


Water

Specific State ID: 5151

(25943 molecules)

H2O


Sodium ion

Specific State ID: 5153

(73 molecules)

Na+