Thanks for the reply, Dr Case.
I'm running AMBER on a cluster and I have no authority to change the
$AMBERHOME/dat/leap/lib files. So is there an easy way to do it locally?
Thanks a lot.
Victor
On Tue, Nov 1, 2011 at 7:14 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Oct 31, 2011, Victor Ma wrote:
> >
> > For atom: .R<Mg+ 1030>.A<Mg+ 1> Could not find type: Mg+
>
> There really isn't any "Amber recommended" parameter set for magnesium,
> although we are working on it.
>
> You can try this:
>
> Go to $AMBERHOME/dat/leap/lib, and edit ions08.cmd
> Change the line
> i = createAtom Mg+ Mg+ 2.0
> to
> i = createAtom Mg+ MG 2.0
>
> The type "tleap -f ions08.cmd"
>
> This will change the atom type of magnesium from "Mg+" to "MG", which
> should
> be recognized by both parm99.dat and parm10.dat, giving you a rather old
> parameter set by Aqvist:
>
> MG 0.7926 0.8947 Mg2+ Aqvist JPC
> 1990,94,8021.(adapted)
>
> Use this with care. If you are a following a literature protocol, you
> might
> check on what magnesium parameters were used there.
>
> ....dac
>
>
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Received on Tue Nov 01 2011 - 08:30:02 PDT
