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Simulation report

Technical information

General information

Name: 6c1q apoform (apoform)

PDB id: 6C1Q

Activation state: Inactive

Description: Classical unbiased (NVT ensemble) complex flexibility assay

Submitted by: Oriol Canal, Universitat Pompeu Fabra

System setup

Solvent type: TIP3P

Membrane type: Homogeneous

Membrane composition: POPC

Ionic composition: Chloride (216 mM), Sodium ion (156 mM)

Number of molecules:

Water: 13144

POPC: 167

Chloride: 51

Sodium ion: 37

C5a anaphylatoxin chemotactic receptor 1: 1

Total number of atoms: 66801

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"

References

David Aranda-García, Tomasz Maciej Stepniewski, Mariona Torrens-Fontanals, Adrian García-Recio, Marta Lopez-Balastegui, Brian Medel-Lacruz, Adrián Morales-Pastor, Alejandro Peralta-García, Miguel Dieguez-Eceolaza, David Sotillo-Nuñez, Tianyi Ding, Matthäus Drabek, Célien Jacquemard, Jakub Jakowiecki, Willem Jespers, Mireia Jiménez-Rosés, Víctor Jun-Yu-Lim, Alessandro Nicoli, Urszula Orzel, Aida Shahraki, Johanna K. S. Tiemann, Vicente Ledesma-Martin, Francho Nerín-Fonz, Sergio Suárez-Dou, Oriol Canal, Gáspár Pándy-Szekeres, Jiafei Mao, David E. Gloriam, Esther Kellenberger, Dorota Latek, Ramon Guixà-González, Hugo Gutiérrez-de-Terán, Irina G. Tikhonova, Peter W. Hildebrand, Marta Filizola, M. Madan Babu, Antonella Di Pizio, Slawomir Filipek, Peter Kolb, Arnau Cordomi, Toni Giorgino, Maria Marti-Solano, Jana Selent.. None. Large scale investigation of GPCR molecular dynamics data uncovers allosteric sites and lateral gateways. None. doi: 2ndround.



Find a list of all simulations published in this paper: GPCRmd publication id 1535

Simulation components

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Open with GPCRmd Workbench

Mutations

No mutations found



Other molecules



Chloride

Specific State ID: 5154

(51 molecules)

Cl-


Water

Specific State ID: 5151

(13144 molecules)

H2O


Sodium ion

Specific State ID: 5153

(37 molecules)

Na+


POPC

Specific State ID: 5152

(167 molecules)


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