Dynarepo 7MHY

Open

Omid Mokhtari;Hamed Khakzad;Yasaman Karami;

MD-A003N7

Created: 23 Jul 2025
License: Apache License 2.0 (opens in a new tab)

Description

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

Molecular system

Starting structure: 7MHYPDB 7MHY(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 chain8,015 atoms491 residues
Total8,015 atoms491 residues
Box dimensions: Dodecahedron
a10.799nm
b10.799nm
c7.63nm

Sequences

Sequence 1Protein · 491 residues

MLPRWELALY LLASLGFHFY SFYEVYKVSR EHEEELDQEF ELETDTLFGG LKKDATDFEW SFWMEWGKQW LVWLLLGHMV VSQMATLLAR KHRPWILMLY GMWACWCVLG TPGVAMVLLH TTISFCVAQF RSQLLTWLCS LLLLSTLRLQ GVEEVKRRWY KTENEYYLLQ FTLTVRCLYY TSFSLELCWQ QLPAASTSYS FPWMLAYVFY YPVLHNGPIL SFSEFIKQMQ QQEHDSLKAS LCVLALGLGR LLCWWWLAEL MAHLMYMHAI YSSIPLLETV SCWTLGGLAL AQVLFFYVKY LVLFGVPALL MRLDGLTPPA LPRCVSTMFS FTGMWRYFDV GLHNFLIRYV YIPVGGSQHG LLGTLFSTAM TFAFVSYWHG GYDYLWCWAA LNWLGVTVEN GVRRLVETPC IQDSLARYFS PQARRRFHAA LASCSTSMLI LSNLVFLGGN EVGKTYWNRI FIQGWPWVTL SVLGFLYCYS HVGIAWAQTY A

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

Files

47 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 7MHY

Description

Molecular system

Sequences

Experiments

Files

Contributors

Acknowledgements