I agree with Dave on these choices. We are working on an updated GB that
will handle protein-dna complexes (igb=8 for nucleic acids). U til then,
follow Dave's advice.
On Jul 31, 2013 7:45 AM, "David A Case" <case.biomaps.rutgers.edu> wrote:
> On Wed, Jul 31, 2013, Catein Catherine wrote:
>
> > However, it is not clear to me the differences between igb=2 or igb=5.
>
> Join the club! I don't think there are any systematic diffs between these
> two
> models. And both are now obsolete. For proteins, my recommendation is to
> use
> igb=8; for nucleic acids, I personally still like igb=1, but opinions
> differ.
> See, e.g.
>
> %A T. Gaillard
> %A D.A. Case
> %T Evaluation of DNA Force Fields in Implicit Solvation
> %J J. Chem. Theory Comput.
> %V 7
> %P 3181-3198
> %D 2011
>
> ...dac
>
>
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Received on Wed Jul 31 2013 - 05:00:03 PDT
