Dynarepo 4LEO

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Omid Mokhtari;Hamed Khakzad;Yasaman Karami;

MD-A003LL

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: 4LEOPDB 4LEO(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 chain9,052 atoms604 residues
Total9,052 atoms604 residues
Box dimensions: Dodecahedron
a14.385nm
b14.385nm
c10.163nm

Sequences

Sequence 1Protein · 604 residues

AVCPGTLNGL SVTGDAENQY QTLYKLYERC EVVMGNLEIV LTGHNADLSF LQWIREVTGY VLVAMNEFST LPLPNLRVVR GTQVYDGKFA IFVMLNYNTN SSHALRQLRL TQLTEILSGG VYIEKNDKLC HMDTIDWRDI VRDRDAEIVV KDNGRSCPPC HEVCKGRCWG PGSEDCQTLT KTICAPQCNG HCFGPNPNQC CHDECAGGCS GPQDTDCFAC RHFNDSGACV PRCPQPLVYN KLTFQLEPNP HTKYQYGGVC VASCPHNFVV DQTSCVRACP PDKMEVDKNG LKMCEPCGGL CPKACEGTGS GSRFQTVDSS NIDGFVNCTK ILGNLDFLIT GLNGDPWHKI PALDPEKLNV FRTVREITGY LNIQSWPPHM HNFSVFSNLT TIGGRSLYNR GFSLLIMKNL NVTSLGFRSL KEISAGRIYI SANRQLCYHH SLNWTKVLRG PTEERLDIKH NRPRRDCVAE GKVCDPLCSS GGCWGPGPGQ CLSCRNYSRG GVCVTHCNFL NGEPREFAHE AECFSCHPEC QPMEGTATCN GSGSDTCAQC AHFRDGPHCV SSCPHGVLGA KGPIYKYPDV QNECRPCHEN CTQGCKGPEL QDCL

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

Files

38 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 4LEO

Description

Molecular system

Sequences

Experiments

Files

Contributors

Acknowledgements