[gmx-users] Protein-protein complex regarding
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.
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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