RGS_Ga_work

This GitHub repository contains the input files for classical molecular dynamics (MD) simulations, including topology files, initial coordinates, and PDB structures of different RGS-Ga complexes. We performed a total of 2 ns simulations for each complex to study their conformational dynamics using the Amber 18 package.

Folder Structure

• input-files

  • Minimization: Files for the minimization steps.
    • min0.in 100 kcal mol^-1Å^-2
    • min1.in 25 kcal mol^-1Å^-2
    • min2.in 20 kcal mol^-1Å^-2
    • min3.in 15 kcal mol^-1Å^-2
    • min4.in 10 kcal mol^-1Å^-2
    • min5.in 5 kcal mol^-1Å^-2
    • min6.in 0 kcal mol^-1Å^-2
  • NVT Heating: Files for the constant volume and temperature (NVT) heating steps.
    • cum_md0.in 0-50 K
    • cum_md00.in 50-100 K
    • cum_md000.in 100-150 K
    • cum_md0000.in 150-200 K
    • cum_md00000.in 200-250 K
    • cum_md000000.in 250-300 K
  • NVT Equilibration: Files for the NVT equilibration steps.
    • cum_md0000000.in 100 kcal mol^-1Å^-2
    • 1cum_md0000000.in 25 kcal mol^-1Å^-2
    • 2cum_md0000000.in 20 kcal mol^-1Å^-2
    • 3cum_md0000000.in 15 kcal mol^-1Å^-2
    • 4cum_md0000000.in 10 kcal mol^-1Å^-2
    • 5cum_md0000000.in 5 kcal mol^-1Å^-2
    • 6cum_md0000000.in 0 kcal mol^-1Å^-2
  • NPT Equilibration: Files for the constant pressure and temperature (NPT) equilibration steps.
    • npt-equil.in 1 µs
  • Production Run: Files for the production run.
    • cum_md1.in 10 ns

• rgs01-ga RGS1-Gα_i1

  • PDB ID: 2GTP
  • Topology: rgs01.parm7
  • Initial Cord: rgs01.rst7

• rgs02-ga RGS2-Gα_i3

  • PDB ID: 2V4Z
  • Topology: rgs02.parm7
  • Initial Cord: rgs02.rst7

• rgs04-ga RGS4-Gα_i1

  • PDB ID: 1AGR
  • Topology: rgs04.parm7
  • Initial Cord: rgs04.rst7

• rgs08-ga RGS8-Gα_i3

  • PDB ID: 2ODE
  • Topology: rgs08.parm7
  • Initial Cord: rgs08.rst7

• rgs09-ga RGS9-Gα_t/i1

  • PDB ID: 1FQK
  • Topology: rgs09.parm7
  • Initial Cord: rgs09.rst7

• rgs10-ga RGS10-Gα_i3

  • PDB ID: 2IHB
  • Topology: rgs10.parm7
  • Initial Cord: rgs10.rst7

• rgs16-ga RGS16-Gα_i1

  • PDB ID: 2IK8
  • Topology: rgs16.parm7
  • Initial Cord: rgs16.rst7

Simulation Details

• Software Used: Amber 18
• Simulation Time: 1 µs for each complex (two times)

These files can be used to replicate the simulations and study the conformational dynamics of RGS-Ga complexes.