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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Received on Sun Nov 18 2007 - 06:07:50 PST
