[gmx-users] Protein-protein complex regarding

Justin Lemkul jalemkul at vt.edu
Mon Apr 30 23:03:17 CEST 2018

On 4/30/18 4:48 PM, RAHUL SURESH wrote:
> Dear all
> I am doing MD simulation of a Protein protein complex docked using Zdock
> server in charmm36 ff. Is it mandatory to treat a protein like a ligand as
> in protein-ligand tutorial and apply position constraint? Or is it fine if
> I simply simulate the complex in solvent without adding any extra terms to
> the top file?

You don't need to treat the protein like a ligand (which in the tutorial 
is a non-protein, small molecule, which requires additional 
parametrization and consideration). pdb2gmx provides a completely 
functional topology. You should apply restraints during equilibration, 
but those will apply to both protein chains.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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