Dynarepo 7SBG

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Omid Mokhtari;Hamed Khakzad;Yasaman Karami;

MD-A003N9

Description

Antigen from SAbDab, Classical MD simulations, 3 replicates of 500 ns

Starting structure: 7SBGPDB 7SBG(opens in a new tab)
Force field: CHARMM36mTIP3P
Engine: GROMACS 2024.2
Method: Classical MD
Ensemble: NPT
Temperature: 310 K
Timestep: 2 fs
Composition: Molecules of interest
ProteinProtein · 1 chain2,004 atoms134 residues
Total2,004 atoms134 residues
Box dimensions: Dodecahedron
a6.972nm
b6.972nm
c4.914nm

1

Sequence 1Protein · 134 residues

DDKMSWQAYV DDHLMCEIEG NHLSAAAIIG QDGSVWAQSA NFPQFKSEEI TGIMSDFHEP GTLAPTGLYI GGTKYMVIQG EPGAVIRGKK GPGGVTVKKT NQALIIGIYD EPMTPGQCNM IVERLGDYLI DQGY

3

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DynaRepo Acknowledgements