[gmx-users] Protein-protein complex regarding

[Justin Lemkul]

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

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

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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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