AMBER Archive (2007)

Subject: AMBER: xleap heme iron coordination error

From: Robyn Ayscue (kajsicat_at_yahoo.com)
Date: Fri Nov 16 2007 - 13:33:35 CST

All:

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')

This is the only error I get regarding the
coordination of the heme iron, and xleap writes the
top and crd files even with the error. There is no
mention of any missing parameters if I tell xleap to
check the molecule, and from a visual perspective it
seems to be fine. I need to run a molecular dynamics
simulation on this enzyme, but I can't do that until I
make sure that the top file xleap is writing here
contains information for a hexacoordinated heme iron,
and not a pentacoordinated iron like this error
suggests.

Has anyone else seen this before? Any suggestions
would be greatly appreciated.

Thanks,
Robyn Ayscue
West Virginia University

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