Hi Norbert,
you might want to look at these articles, both describe simulations of Fpg
with FapydG, with parameters too.
Song, K., Hornak, V., de los Santos, C., Grollman, A. and Simmerling,
C., “*Molecular
Mechanics Parameters for the FapydG DNA lesion*”, J. Comput. Chem., 9:17
(2007)
Song, K., Kelso, C., de los Santos, C., Grollman, A. and Simmerling,
C., “*Molecular
simulations reveal a common binding mode for glycosylase binding of
oxidatively damaged DNA lesions*”. J. Am. Chem. Soc., 129:14536 (2007)
and here is a more recent one, also on Fpg:
Bergonzo, C., Campbell, A., de los Santos, C., Grollman, A and Simmerling,
C. “Energetic Preference of 8-oxoG Eversion Pathways in a DNA Glycosylase”,
J. Am. Chem. Soc., 133, 14504–14506 (2011)
best,
Carlos
On Wed, May 7, 2014 at 8:30 AM, Norbert GARNIER <
norbert.garnier.cnrs-orleans.fr> wrote:
> Dear AMBER users,
>
> Using AMBER 11, I would like to perform MD simulations on a Fpg/DNA
> complex including a FapydG nucleotide (PDB 1XC8).
> Could you give me some advice on procedures for determining atomic
> partial charges as well as the corresponding force field parameters
> (xx.frcmod)?
> Thank you very much for your help.
> Best regards,
>
> Norbert
>
> --
> Dr. Norbert GARNIER
> Maître de Conférences
> Université d'Orléans, Orléans France
>
> « DNA repair: structural and functional approaches»
> Centre de Biophysique Moléculaire, UPR4301, CNRS
> rue Charles Sadron
> 45 071 Orléans cedex 02
> Tel: +33 (0)2 38 25 76 68
> Web site : http://cbm.cnrs-orleans.fr/
>
>
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Received on Wed May 07 2014 - 07:00:04 PDT
