On Wed, Sep 5, 2012 at 6:35 AM, Thomas Gaillard <
thomas.gaillard.polytechnique.edu> wrote:
> Le Tuesday 04 September 2012 à 10:31:10PM, jit mukherjee a écrit :
> > Dear Carlos,
> > Thanks for your reply. You advised me to use igb=1 only. Why only igb=1
> and
> > not igb=2 (igb=2 is better than igb=1 to describe true molecular volume,
> > i.e. , closer to real situation than using igb=1). Is the effective Born
> > radii are not rescaled for nucleic acid or the corresponding bases?
> Please
> > clarify.
> >
> > Regards,
> > jit
>
> Hi,
>
> You can maybe have a look at the following work, where different GB
> variants
> (AMBER GB 1, 2, 5, 7; CHARMM GBMV) in combination with both ff99bsc0 and
> all27 force fields were evaluated for DNA modeling against explicit
> simulation and experimental data:
>
> Evaluation of DNA Force Fields in Implicit Solvation
> J. Chem. Theory Comput., 2011, 7, 3181
> http://dx.doi.org/10.1021/ct200384r
>
> - FF and GB defects can compensate or add up
>
> - best FF+GB combinations are ff99bsc0+GBMV ("AMBARMM") or all27+GB1
> ("CHAMBER")
>
> - GBMV is better than pairwise GB methods
>
> - GB1 is better than GB 2, 5, 7
>
>
> AMBER GB8 was not tested.
>
> just want to add comment to Gaillard's work: GB8 model does not have
parameters for nucleic acid yet. We don't recommend to use this model in
current status for DNA/RNA duplex and others since it just make two strands
fall apart like GB7 does.
Hai Nguyen
> --
> Thomas Gaillard
> Maître de conférences
> Laboratoire de Biochimie
> Ecole Polytechnique
> 91128 Palaiseau cedex
> tel: +33 1 69 33 48 62
> fax: +33 1 69 33 49 09
> thomas.gaillard.polytechnique.edu
> http://bioc.polytechnique.fr/~gaillard
>
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Received on Wed Sep 05 2012 - 10:00:04 PDT
