[gmx-users] Protein-Ligand Complex MD simulation: Restrain protein alone or Restrain both protein and ligand during simulation?
zebamir85 at gmail.com
Thu Dec 22 06:54:02 CET 2016
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Everything will go fine
On Wed, Dec 21, 2016 at 8:50 PM, Adarsh V. K. <adarsh_p130085bt at nitc.ac.in>
> 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
> 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 to
> *.pdb and view in Pymol?
> Adarsh V. K.
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