Dynarepo 4ZPT

Open

Omid Mokhtari;Hamed Khakzad;Yasaman Karami;

MD-A003LU

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: 4ZPTPDB 4ZPT(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 chain3,187 atoms208 residues
Total3,187 atoms208 residues
Box dimensions: Dodecahedron
a8.94nm
b8.94nm
c6.275nm

Sequences

1

Sequence 1Protein · 208 residues

VECDFSPLLS GTPPQVYNFK RLVFTNCNYN LTKLLSLFSV NDFTCSQISP AAIASNCYSS LILDYFSYPL SMKSDLSVSS AGPISQFNYK QSFSNPTCLI LATVPHNLTT ITKPLKYSYI NKCSRFLSDD RTEVPQLVNA NQYSPCVSIV PSTVWEDGDY YRKQLSPLEG GGWLVASGST VAMTEQLQMG FGITVQYGTD TNSVCPKL

Experiments

3

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

Contributors

Research groups: Delta team, Inria center at the University of Lorraine
Contact: yasaman.karami@inria.fr

Acknowledgements

DynaRepo Acknowledgements