AMBER Archive (2007)

Subject: Re: AMBER: xleap heme iron coordination error

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On Fri, Nov 16, 2007, Robyn Ayscue wrote:
>
> I'm trying to model a P450 enzyme with an oxoheme in
> Amber8. The problem I'm having is that the heme iron
> is hexacoordinated, but in xleap when I save a top and
> crd file of the protein with the heme it complains
> that the iron is pentacoordinated:
>
> (FE: unexpected coordination 5 - using nonstandard
> tree type '5')

I'm pretty sure that this is just a warning: LEaP wants you to know that you
have a "unexpected" (unusal) coordination, and what it thinks is the
coodination may not be what a chemist would call it. You can use the "desc"
command in LEaP to be sure that you really have 6 bonds to iron. Plus, run
some short simulations and examine the heme visually to make sure it is doing
what you want.

...good luck....dac

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