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

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

2016-12-21 Thread 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. wrote: > Dear all, > > We have a 419 amino acid long protein and planned Protein-ligand complex MD > s

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

2016-12-21 Thread 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. 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