[gmx-users] Protein-Ligand Complex MD simulation

[Adarsh V. K.]

Dear all,


We have a 419 amino acid long protein and planned 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
nanosecond 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.