[gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Jorden Cabal]

Hi Amit,
The metal ion needs to be treated very very carefully so as to maintain
their co-ordination state with the nearby atoms of protein.
To do this, one needs to generate the parameter separately for the complex
formed by the metal ion with the protein residues because due to presence
of metal ion in the vicinity, the residues nearby will have different
parameters than other proteins especially the charge distribution. One
method of incorporating this model is to model the metal ion as a
dummy-particle metal ion complex model where the dummy particles carry some
partial charge and the whole complex represent the co-ordination state of
that particular atom.
I would suggest you to go through this paper
https://pubs.acs.org/doi/pdf/10.1021/jp501737x

In case, you do not want to go in that much detailed modeling of metal ion
for your system, which I think is very important to study metalloproteins,
another very simple method of solving the problem you are facing is to
treat metal ions as single sphere as you are treating in your system. To
avoid its displacement from its location, you need to apply some distance
restraints which is very easy to apply in Gromacs.
You can create the distance restraint using "*genrestr*" command. Please
note that applying any kind of restraint will definitely add some bias to
your simulation.
Thank you

On Thu, Oct 10, 2019 at 1:05 PM Amit Jaiswal <amitjai20 at yandex.com> wrote:

> Hello Everyone,
>
> Would you please let me know what should we do when the zinc ion gets
> displaced during simulation of a Protein-Zn-Ligand complex? What are the
> possible options one can perform under such conditions? If possible, please
> mention the steps needed to be performed briefly as i am new to GROMACS.
> Your suggestions will help me a lot and thanks in advance.
>
> With kind regards,
> Amit
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