Dynarepo 5D71

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Omid Mokhtari;Hamed Khakzad;Yasaman Karami;

MD-A003LY

Description

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

Starting structure: 5D71PDB 5D71(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 chain1,827 atoms114 residues
Total1,827 atoms114 residues
Box dimensions: Dodecahedron
a6.977nm
b6.977nm
c4.949nm

1

Sequence 1Protein · 114 residues

STQPWEHVNA IQEARRLLNL SRDTAAEMNE TVEVISEMFD LQEPTCLQTR LELYKQGLRG SLTKLKGPLT MMASHYKQHC PPTPETSCAT QIITFESFKE NLKDFLLVIP FDCW

3

43 files

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DynaRepo Acknowledgements