[gmx-users] Re: Parameterization of a molecule containing a radical, (oxygen) (Justin A. Lemkul)

Gerrit Groenhof ggroenh at gwdg.de
Wed Mar 23 08:18:04 CET 2011

There is a AMBER FF for this kind of nitroxide spin labels. See PCCP 12 
(2010) 11697.

Hope it helps,

> 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.

> -Justin
>> -- 
>> Simone Cirri

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