Dear Ankita,
Using weak NMR restraints should work to keep the ion in place for the minimization…
BUT,
Even tough you *can* use some weak restraints to hold the Zn ion in place, if you plan to run other simulations on this system, I suspect the real question you need to address is *why* the ion is leaving the position.
I suggest that you look into other simulations of metalloproteins before continuing. Depending on your system, there are cases where the Zn ion can be treated simply as the Zn2+ ion, but there also cases where you may need to reparameterize parts of the system to consider bonds with the Zn Ion, and only you can make this decision.
—
Gustavo Seabra.
> Em 12 de fev de 2016, à(s) 08:03, ankita mehta <mehtaroadies.gmail.com> escreveu:
>
> Dear All,
>
> I want to minimize a protein which contains Zn ion.
> But the problem is Zn ion is displacing from the position after
> minimization!
> Can u suggest the way through which position of Zn ion can be fixed.
> i am attaching t he leap.log file and min.out file..
> please suggest the way out!
>
> I shall be thankful!
> <leap.log><min-solvation-12-6-4.out>_______________________________________________
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Received on Fri Feb 12 2016 - 06:30:03 PST
