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

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 23 01:56:41 CET 2011

Simone Cirri wrote:
> 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 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994&loc=ec_rcs 
> <http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994&loc=ec_rcs>
> 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.
> <http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994&loc=ec_rcs>

This would not be a trivial molecule to parameterize.  You could start by using 
antechamber (available free as part of AmberTools), since it allows you to tune 
multiplicity (-m flag).  Otherwise, the existing force fields may not provide a 
suitable atom type for the O radical or its effects on the rest of the molecule. 
  I still don't know if parameterization would be possible for a standard MM 
force field (though it very well might), but this might get you started.


> -- 
> Simone Cirri


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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