[gmx-users] Parameterization of a molecule containing a radical (oxygen)

Simone Cirri simonecirri at gmail.com
Tue Mar 22 16:21:05 CET 2011

Hi all,
I have a question regarding a new parameterization: actually, I'm wondering
whether or not it is possible to do it.

The molecule is tempol; you cand find its PubChem entry here
As you can see, the problem of this molecule is its O radical; this, and the
N belonging to the cycle too.
My lab would really benefit from the parameterization (for the AMBER force
field) of tempol, since we commonly use it in our NMR experiments. We don't
know how to treat the oxygen radical and the N bound to it, though.
If this parameterization is impossible to do we will give up, but we would
like to be sure about it.
Thanks in advance for any answer you could provide.

Simone Cirri
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