Re: [AMBER] Zn active site parameterization

From: Per Jr. Greisen <>
Date: Mon, 7 Mar 2011 14:12:30 +0100


I do not know if you already figured out a solution for your problem
but you could use the restraint within amber to fix your metal ion in
this case Zn - would this be the proper way to treat a metal site?

You could consult this page for suggestions on treating metal sites


On Sun, Mar 6, 2011 at 8:59 PM, kala <> wrote:
> Dear friends.
>                 I am new to amber MD and I am working on a terinery complex
> simulation. There is a ZN2+ ion at the active site coordinately bonded to
> HISD, ASP and CYS and also with a drug molecule of interest. I need to
> restrain the bonds and maintain the charge on the ion. This was quite easy
> in gromacs, where in we can specify them in specbond.dat and parameters for
> Zn are automatically calculated. but this is not the case using with tleap
> and antechamber ( found a tutorial of rosswalker
> but
> this is quite outdated and doesnt work well with amber11's tleap). I Need to
> perform simulations on a set of docked complexes. I have a fermi card and
> md-run in gromacs is not quite evolved as pmemd.cuda. Any help is highly
> appreciated.
> thanks and regards
> bharath
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Received on Mon Mar 07 2011 - 05:30:05 PST
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