Dynarepo 7LO6

Open

Omid Mokhtari;Hamed Khakzad;Yasaman Karami;

MD-A003IX

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: 7LO6PDB 7LO6(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 chain7,282 atoms469 residues
Total7,282 atoms469 residues
Box dimensions: Dodecahedron
a13.661nm
b13.661nm
c9.651nm

Sequences

Sequence 1Protein · 469 residues

NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNVWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHTDIISLW DQSLKPCVKL TPLCVTLQCT NVTNNITDDM RGELKNCSFN MTTELRDKKQ KVYSLFYRLD VVQINENQGN RSNNSNKEYR LINCNTSAIT QACPKVSFEP IPIHYCAPAG FAILKCKDKK FNGTGPCPSV STVQCTHGIK PVVSTQLLLN GSLAEEEVMI RSENITNNAK NILVQFNTPV QINCTRPNNN TRKSIRIGPG QAFYATGDII GDIRQAHCTV SKATWNETLG KVVKQLRKHF GNNTIIRFAN SSGGDLEVTT HSFNCGGEFF YCNTSGLFNS TWISNTSVQG SNSTGSNDSI TLPCRIKQII NMWQRIGQAM YAPPIQGVIR CVSNITGLIL TRDGGSTNST TETFRPGGGD MRDNWRSELY KYKVVKIEPL GVAPTRAKR

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

Files

51 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 7LO6

Description

Molecular system

Sequences

Experiments

Files

Contributors

Acknowledgements