[gmx-users] Re: Zn-NE2 bond restraint

[Wei Fu]

Thanks for your response. Yes, Zn is only structural. However, I would like to know how to deal with the case if Zn coordinated with some groups  (like -COO) of ligand? add force on both Zn and ligand-COO? Thanks.

Linda

> Dear David,
>  
>     Thanks so much for your reply on Zn - His-NE2 restraint.
>  
>       You told me to restrain the bonds between zinc and two His-NE2
> for the zinc protease MD simulation, however, I would like to make
> sure 
> whether I correctly set up the restraint, so that I can SAFELY perform
> the production run. I simply added force on three atoms: Zn and two
> His-NE2, is this OK?? 
There are probably more ligands for the Zn?
ANyway if the Zn is only structural this is fine.
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