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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 01 2011 - 05:30:07 PDT
