Example of molecular dynamics simulations analyzed with the Bios2cor package
Description
This dataset provides all the data necessary to analyze correlated sidechain motions in an accelerated molecular dynamics trajectory of CXCR4 with the bios2cor package. It includes: (1) the raw trajectory with input and parameters files, (2) 25 snapshots of the trajectory in pdb format, (3) all the data for the Bios2cor analysis and (4) an excel file with equivalence between CXCR4 numberings.
Files
Steps to reproduce
The CXCR4 model with bound sodium was built with MODELLER 9v8 from the crystal structures of CXCR4 (PDB ODU) and OPRD (PDB 4N6J). The receptor model was embedded in a POPC lipid bilayer, hydrated and charge neutralized withe the CHARMM-GUI interface. Molecular dynamics simulations were run with the NAMD v2.9 MD software using the CHARMM36 forcefield. A preliminary 120ns classical MD trajectory was run to determine the acceleration thresholds. The acceleration parameter was set at 0.3. The detailed protocol is identical to that described in Taddese et al. (2018) Plos Comput Biol 14(6):e1006209. doi: 10.1371/journal.pcbi, except that the simulations were run on the E-biothon cloud platform.