[gmx-users] Oh topology .. go away ...

[Marc Baaden]

Sorry to continue bothering you with my topology questions,
but I think this one is quite interesting.

I have a structure with iron in an environment of 6 oxygens.
Test of ionic vs covalent model indicate that the covalent
model is better.

But, in fact the 6 oxygens are part of 3 aromatic rings, and
I would like them to adopt a "twisted" configuration, which
should come naturally from the O-O LJ and electrostatic repulsion. 

As I have my Fe bonded to the oxygens, they are now in a 1-3
position with respect to each other and thus have no LJ
interaction ! The result is a perfectly planar coordination
environment of the Fe, which is wrong for this particular
molecule.
So how can I INCLUDE LJ and electrostatic terms for these
"1-3 bonded" oxygens only  ?

NB: The iron is involved in Fe-O bond, Fe-O-C angle and Fe-O-C-C
    dihedral terms


  Marc

-- 
 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
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