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.
--
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 - 04:00:03 PDT
