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
--
========================================
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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