Constant-pH MD and standard MD simulations of the plant transporter GTR1/NPF2.10

This dataset contains input files, trajectories (1 frame every ns), force field parameters, and analysis output from the molecular dynamics (MD) and Constant-pH MD (CpHMD) simulations supporting the manuscript: Yoon, G.-Y., Kim, U., Kanstrup, C., Pasquadibisceglie, A., Steffen, J. H., de Prado Parralejo, V., Crocoll, C., Mirza, O., Delemotte, L., Cho, H.-S., Nour-Eldin, H. H. & Gourdon, P. Molecular basis of glucosinolate binding and translocation in plant GTR1/NPF2.10. [Journal Name, Year]. DOI: [to be added upon acceptance] Folder content: ├── GTR1A_OF_cph5.5/ - Apo outward-open, CpHMD at pH 5.5 ├── 0_system/ - System setup files (starting structure, topology, mdps) ├── charmm36-mar2019-cphmd.ff/ - CpHMD-specific force field ├── MD1/ Replica 1 ├── MD2/ Replica 2 ├── MD3/ Replica 3 └── CouplingAnalysis/ - SVM / mutual-information analysis of E75, E78 |── GTR1A_IF_cph7.5/ - Apo inward-open, CpHMD at pH 7.5 ├── 0_system/ ├── charmm36-mar2019-cphmd.ff/ ├── MD1/ ├── MD2/ └── MD3/ ├── GTR1I_IF_cph6/ - I3M-bound inward-open, CpHMD at pH 6.0 ├── 0_system/ ├── charmm36-mar2019-cphmd.ff/ ├── MD1/ ├── MD2/ └── MD3/ |── GTR1I_IF_E513p/ - Standard MD, I3M-bound inward-open, E513 protonated ├── 0_system/ - Shared system setup files (topology, MDP, toppar) ├── MD1/ ├── MD2/ └── MD3/ |── GTR1I_IF_E513d/ - Standard MD, I3M-bound inward-open, E513 deprotonated ├── 0_system/ ├── MD1/ ├── MD2/ └── MD3/ |── RMSDD/ - Python scripts to reproduce the RMSDD analysis performed on GTR1A_OF_cph5.5 and GTR1A_IF_cph7.5 trajectories