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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 20 2009 - 16:42:20 PDT
