DynaRepo 7CQC

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Omid Mokhtari;Hamed Khakzad;Yasaman Karami;

MD-A003NF

Description

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

Starting structure: 7CQCPDB 7CQC(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 · 3 chains2,995 atoms186 residues
Total2,995 atoms186 residues
Box dimensions: Dodecahedron
a8.72nm
b8.72nm
c6.136nm

3

Sequence 1Protein · 14 residues

EGGVAMPGAE DDVV

Sequence 2Protein · 65 residues

VPKYLKEPVV VGYVQRDSIA QKIGIKPGDK IIKIGYEVRT WEDLRDALIR LSLDGVKETT LFLER

Sequence 3Protein · 107 residues

EVLHLTIKVP NVQKGEELGI APLVKPVVGG VKKGSPADQV GIKPGDLILE VNGKKINTWY ELVEEVRKSQ GKAIKLKILR NGKMIEKELI PAKDPKTGTY FIGLFPK

3

104 files

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DynaRepo Acknowledgements