[gmx-users] Protein-Ligand Complex MD simulation

[Adarsh V. K.]

  We have a 419 amino acid long protein and planned for Protein-ligand
complex
    MD simulation using Gromacs 5.1.4 to check.

    —Whether the protein and inhibitor complex stable

    —Did the inhibitor remain in the active site pocket or did it fall out
    during the simulation

    —What factors contributed to the stability - hydrogen bonds or other
    interactions.

     1. What sought of MD simulation we have to perform?. Is it ok a two
    nanosec simulation?.

     2. Restrain protein alone or Restrain both protein and ligand during
    simulation?.

     3. What is the exact command for Drug positional RMSD plot?

     4. What is the exact command for Number of Hydrogen bond plot?

     5. What is the exact command for Other interactions between protein and
    ligand?

     6. how to view the trajectory files? or We have to convert the frames
to
    *.pdb and view in Pymol?

    Regards,

    Adarsh V. K.