Molecular dynamics studies of HrcQb

This project is in collaboration with IMBB, FORTH. Person responsible : Dr Vasiliki E. Fadouloglou (fadoulog@imbb.forth.gr)

• Getting started
  • Force field
  • Create the files needed

• Simulation of native HrcQb
  • heating-up NAMD script
  • equilibration NAMD script
  • equilibration graphs

• Simulation of HrcQb-like FliN? (tetramer)
  • [heating-up NAMD script for FliN 4mer]?
  • [equilibration NAMD script for FliN 4mer]?
  • equilibration graphs for FliN 4mer

• Simulation of the AD HrcQb dimer
  • Heating-up NAMD script for HrcQb dimer

• Simulation of the BC HrcQb dimer
  • [heating-up NAMD script for BC 2mer]?
  • [equilibration NAMD script for BC 2mer]?
  • [equilibration graphs for BC 2mer]?

• Simulation of native FliN? (dimer)
  • [heating-up NAMD script for FliN 2mer]?
  • [equilibration NAMD script for FliN 2mer]?
  • [equilibration graphs for FliN 2mer]?

• Simulation of T40I-HrcQb
  • heating-up NAMD script for T40I
  • equilibration NAMD script for T40I
  • equilibration graphs for T40I

• Simulation of T40Y-HrcQb
  • heating-up NAMD script for T40Y
  • equilibration NAMD script for T40Y
  • equilibration graphs for T40Y

• Simulation of T40W-HrcQb
  • heating-up NAMD script for T40W
  • equilibration NAMD script for T40W
  • equilibration graphs for T40W

• Simulation of I41W-HrcQb
  • [heating-up NAMD script for I41W]?
  • [equilibration NAMD script for I41W]?
  • [equilibration graphs for I41W]?

• Comparative analysis
  • Ca-rmsd as a function of frame. Alignment based on 4mer
  • Ca-rmsd as a function of frame. Alignment based on 2mer
  • Average rmsd for each residue
  • Radius of gyration