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

[Justin A. Lemkul]

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 

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.



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



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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

[Simone Cirri]

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
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
-- 
gmx-users mailing listgmx-users@gromacs.org
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