[gmx-users] Protein-Ligand Complex MD simulation: Restrain protein alone or Restrain both protein and ligand during simulation?

[Amir Zeb]

Hello,

You may follow "
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/
"
Everything will go fine

Good luck

Amir

On Wed, Dec 21, 2016 at 8:50 PM, Adarsh V. K. <adarsh_p130085bt at nitc.ac.in>
wrote:

> Dear all,
>
> We have a 419 amino acid long protein and planned Protein-ligand complex MD
> simulation using Gromacs 5.1.4 to check.
>
>  1. What sought of MD simulation we have to perform?.
>  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.
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