[gmx-users] Should Cation Ligand be removed before MD simulaiton

[Justin Lemkul]

On 8/25/19 10:06 AM, Quin K wrote:
> Hi
>
> I'm hoping to use a protein for MD simulation and later for docking with
> Autodock vina.
>
> *However there is a  Mg2+ cation ligand in the DPB crystal structure of
> protein. Should this be removed before MD simulation? *and replaced with
> lets say Na+ to keep the charge of protein zero.

There is no requirement that the net charge of a protein or complex be 
zero. Usually Mg2+ are structurally or functionally relevant. You need 
to determine what the biological reality of your system is. Don't just 
eliminate an important ion ad hoc; it could be quite important for your 
results.

-Justin

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Justin A. Lemkul, Ph.D.
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