[gmx-users] Simulation of Protein-Protein Complex

[Justin Lemkul]

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.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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