Dynarepo 7NA9

Open

Omid Mokhtari;Hamed Khakzad;Yasaman Karami;

MD-A003J8

Created: 22 Jul 2025
License: Apache License 2.0 (opens in a new tab)

Description

Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns

Molecular system

Starting structure: 7NA9PDB 7NA9(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 chain7,153 atoms440 residues
Total7,153 atoms440 residues
Box dimensions: Dodecahedron
a10.146nm
b10.146nm
c7.196nm

Sequences

Sequence 1Protein · 440 residues

PVTINNFNYN DPIDNNNIIM MEPPFARGTG RYYKAFKITD RIWIIPERYT FGYKPEDFNK SSGIFNRDVC EYYDPDYLNT NDKKNIFLQT MIKLFNRIKS KPLGEKLLEM IINGIPYLGD RRVPLEEFNT NIASVTVNKL ISNPGEVERK KGIFANLIIF GPGPVLNENE TIDIGIQNHF ASREGFGGIM QMKFCPEYVS VFNNVQENKG ASIFNRRGYF SDPALILMHE LIHVLHGLYG IKVDDLPIVP NEKKFFMQST DAIQAEELYT FGGQDPSIIT PSTDKSIYDK VLQNFRGIVD RLNKVLVCIS DPNININIYK NKFKDKYKFV EDSEGKYSID VESFDKLYKS LMFGFTETNI AENYKIKTRA SYFSDSLPPV KIKNLLDNEI YTIEEGFNIS DKDMEKEYRG QNKAINKQAY EEISKEHLAV YKIQMCKSVK

Run	Outputs
replica 1	Trajectory Analyses
replica 2	Trajectory Analyses
replica 3	Trajectory Analyses

Files

46 files

All files

trajectory.binBIN
pca_trajectory_01.binBIN
pca_trajectory_02.binBIN
pca_trajectory_03.binBIN
pca_trajectory_04.binBIN
pca_trajectory_05.binBIN
pca_trajectory_06.binBIN
pca_trajectory_07.binBIN
pca_trajectory_08.binBIN
pca_trajectory_09.binBIN

Dynarepo 7NA9

Description

Molecular system

Sequences

Experiments

Files

Contributors

Acknowledgements