AMBER Archive (2009)

Subject: Re: [AMBER] FE: unexpected coordination 4 - using nonstandard tree type '4'

• Previous message: Chih-Ying Lin: "[AMBER] how to make the different/specific displacement of ligand around protein?"
• In reply to: ben rodriguez: "[AMBER] FE: unexpected coordination 4 - using nonstandard tree type '4'"
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On Fri, May 15, 2009, ben rodriguez wrote:
>
> Hi all, I am triyng to run dynamics on a deoxy heme protein using a
> heme-his residue. When building the topology file I get the following
> message about the Fe coordination. Can anyone explain what this message
> means, and if this is appropriate for deoxy heme simulations. I am using
> ff99SB.
>
> (FE: unexpected coordination 4 - using nonstandard tree type '4')

I think this is OK...check the bonds that your iron has and make sure that it
is correct. The warning per se is not a problem -- it is just telling you
that iron coordination is "unexpected", i.e. not like usual organic atoms.
But you already knew that....

...dac

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• Previous message: Chih-Ying Lin: "[AMBER] how to make the different/specific displacement of ligand around protein?"
• In reply to: ben rodriguez: "[AMBER] FE: unexpected coordination 4 - using nonstandard tree type '4'"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]