Archive File Tree

DecodingCholesterolBindingInTRPV3ThroughComputerSimulation
├── CG
│   ├── runfiles
│   │   ├── minimization_steep.mdp
│   │   ├── npt.mdp
│   │   └── production.mdp
│   ├── trpv6_closed
│   │   ├── itp_files
│   │   │   └── Protein_0.itp
│   │   ├── pdb_files
│   │   │   ├── trpv6_protein_cg.pdb
│   │   │   └── trpv6_protein.pdb
│   │   └── top_files
│   │       └── trpv6_protein.top
│   └── trpv6_open
│       ├── itp_files
│       │   └── Protein_0.itp
│       ├── pdb_files
│       │   ├── trpv6_protein_cg.pdb
│       │   └── trpv6_protein.pdb
│       └── top_files
│           └── trpv6_protein.top
└── SILCS
    ├── HotSpots
    │   ├── chol1-gaussian.mol2
    │   └── hotspots_params.inp
    └── Simulations
        ├── trpv6_closed.pdb
        └── trpv6_open.pdb

File Descriptions

The coarse grain directory (CG) contains the gromacs parameters files, all atom pdb file, the converted all atom pdb file to martini3 coarse grain, and the topology files for the coarse-grained structures.

The SILCS directory contains the PDBs used to run SILCS in both the open and closed states, the mol2 representation of cholesterol used during SILCS Hotspots, and the hotspots parameter file used to run SILCS hotspots.

Acknowledgements

We thank the Red Española de Supercomputación (RES) for providing computational resources via the BSC. We acknowledge the EuroHPC Joint Undertaking for awarding this project access to the EuroHPC supercomputer LUMI at CSC. This project made use of time on HPC granted via the UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim (http://hecbiosim.ac.uk), supported by EPSRC (grant no. EP/X035603/1). We acknowledge support from the International Human Frontier Science Program Organization (HFSPO), grant number RGP023/2024.