BioSimDB
Published June 2025 | Version v1
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Beta2 adrenergic receptor in the presence of 10% of benzamide (BZA) 40 ns

Creators

  • 1. Queens University Belfast

Description

Probe MD simulations. Mapping an allosteric site at the intracellular side of the Beta2 adrenergic receptor. Beta2 adrenergic receptor in the presence of 10% of benzamide (BZA) in the water-POPC bilayer. 0.15M of Na+ and Cl-. Three replicates are provided.

Trajectory originally donated to SlimMD

Files

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md5:b90083e88f89bb5dff99acb582d9e85c
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Additional details

Identifiers

DOI
10.1021/acscentsci.1c00802

Domain Specific Metadata

 
Property Value
Software NAMD
Software Version Git-2017-12-19
Molecular Model atomistic
Simulation Method classical
Timestep 2 femtosecond
Framestep 0.2 nanoseconds
Length 0.04 microseconds
Temperature 310 K
Pressure 1.01325 bar
Ensemble NPT
Box Type cubic
Trajectories Cartesian coordinates
Force Fields CHARMM36, CgenFF v1.0.0
Experimental Structures https://www.rcsb.org/structure/5X7D
Membrane Yes
Ligands https://pubchem.ncbi.nlm.nih.gov/compound/Benzamide
Sequences VWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYANETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLQKIDRRSSKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCL
Box Dimensions 72.3 x 84.0 x 173.1 Angstrom, alpha: 90.0, beta: 90.0, gamma: 90.0 degrees
Long Range Cutoff 12 Angstrom
Thermostat langevin
Barostat langevin
Atom Count 108165