Dear Profs Case and Simmerling,
Thanks for your comments. It seems to me that we can only use igb=2 or igb=5 when we do the calculation on per residue decomposition energy analysis.
Can I also use igb=8 or igb=1 for decomposition energies?
Thanks for the reference paper, we shall study it in more details. Thanks a lot.
Best regards,
Catherine.
> Date: Wed, 31 Jul 2013 07:47:38 -0400
> From: carlos.simmerling.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] MM-GBSA igb=2 or igb=5? [Ref: Exploring Protein Native States and Large-Scale Conformational Changes With a Modified Generalized Born Model]
>
> 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 - 21:30:03 PDT
