On 4/2/20 3:19 PM, Surya Sanjay wrote:
Hello all, I am a beginner Gromacs user and I have been using the Gromacs tutorials on mdtutorials.com/gmx/. I would like to simulate the binding of the infectious and normally-folded prion variants, and I want to know if the protein-protein complex procedure is different from that of protein-ligand systems.
A system containing several proteins is functionally no different than simulating one protein. Don't equate protein-protein systems to protein-ligand systems, which often require external ligand parametrization. None of that is necessary when dealing with proteins.
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