Simulation report

Technical information

General information

Name: Mu-type opioid receptor in complex with bu72

PDB id: 5C1M.A

Activation state: Active

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 (155 mM), Chloride (219 mM)

Number of molecules:

Water: 13948

POPC: 177

Chloride: 55

Sodium ion: 39

(2s,3s,3ar,5ar,6r,11br,11cs)-3a-methoxy-3,14-dimethyl-2-phenyl-2,3,3a,6,7,11c-hexahydro-1h-6,11b-(epiminoethano)-3,5a-methanonaphtho[2,1-g]indol-10-ol: 1

Mu-type opioid receptor: 1

Total number of atoms: 70461

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: 1.25 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

Receptor

PDB id: 5C1M.A
Mu-type opioid receptor

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Mutations

No mutations found



Other molecules



Sodium ion

Specific State ID: 5016

(39 molecules)

Na+


Chloride

Specific State ID: 5017

(55 molecules)

Cl-


POPC

Specific State ID: 5018

(177 molecules)


Water

Specific State ID: 5019

(13948 molecules)

H2O


(2s,3s,3ar,5ar,6r,11br,11cs)-3a-methoxy-3,14-dimethyl-2-phenyl-2,3,3a,6,7,11c-hexahydro-1h-6,11b-(epiminoethano)-3,5a-methanonaphtho[2,1-g]indol-10-ol (orthosteric lig.)

Specific State ID: 5102

(1 molecule)