[gmx-users] refinement of homology-based protein structure

[Mahboobeh Eslami]

Hi

I hope you are very well

I designed one protein by Homology modelling approach. I want to use this protein as receptor in docking process. I think that, before docking process, initial designed protein must be refined by MD simulation. How much time should this simulation be done for refinement of homology-based protein structure. What parameters should be monitored to ensure that the time simulation is sufficient.

thanks for your help

best