Molecular Dynamics Trajectories of MMP-9 in Complex with Small-Molecule Inhibitors (IN-01 to IN-06) and Compound_A

This repository contains 100 ns molecular dynamics (MD) trajectories of Matrix Metalloproteinase-9 (MMP-9) in complex with seven small-molecule ligands (Compound_A and inhibitors IN-01 through IN-06). For each ligand-protein complex, three independent simulation replicates (Run1, Run2, Run3) were performed to ensure reproducibility and adequate conformational sampling. Simulations were conducted using AMBER, with trajectory and topology files provided for each run. Each ligand subdirectory contains three independent 100 ns MD trajectories (Run1-Run3) of the corresponding ligand bound to MMP-9. .nc files — AMBER NetCDF format MD trajectory files containing the 100 ns simulation coordinates. .parm7 files — AMBER parameter/topology files describing the system. Usage: These files can be loaded and analyzed using standard MD analysis tools such as AmberTools, VMD etc., by pairing each .nc trajectory file with its corresponding .parm7 topology file. Repository Structure MD_MMP9/├── Compound_A/│ ├── Run1/│ ├── Run2/│ └── Run3/├── IN_01/│ ├── Run1/│ ├── Run2/ (Run2.nc, Run2.parm7)│ └── Run3/├── IN_02/├── IN_03/├── IN_04/├── IN_05/└── IN_06/