Thanks a lot.
I have these papers but I don't know how to modify the ff99 force field
with your new based torsion parameters for rotation about the C5-N7 and
N7-C8 bonds.
Could you please also provide me an example of frcmod file.
Thank you very much.
Best regards,
Norbert
Le 07/05/2014 15:54, Carlos Simmerling a écrit :
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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--
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 - 07:30:06 PDT
