[gmx-users] Protein-Ligand Complex MD simulation

Adarsh V. K. adarsh_p130085bt at nitc.ac.in
Fri Dec 16 05:55:09 CET 2016

  We have a 419 amino acid long protein and planned for Protein-ligand
    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

     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

     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

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


    Adarsh V. K.

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