Hi
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
http://q4md-forcefieldtools.org/RED/
Hth
On Sun, Mar 6, 2011 at 8:59 PM, kala <kalabharath.gmail.com> 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
> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/section1.htm
> 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 this is quite outdated and doesnt work well with amber11's tleap).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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--
Per
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Received on Mon Mar 07 2011 - 05:30:05 PST
