i want to clarify this response a little.
Amber 11 wont have new intrinsic radii, but will have a new GB model for
calculating effective radii. For explicit water calculations, the radii are
not used so it does not matter if you use mbondi or mbondi2. The quality of
PB vs. GB involves more than just radii, but like GB it can be very
sensitive to intrinsic radii as well, and one should follow similar work in
the literature as a guide.
On Sun, Mar 21, 2010 at 4:29 PM, Kevin Hauser <84hauser.gmail.com> wrote:
> Hi, S. Bill,
>
>
> The mbondi (and mbondi2) variables are usually only pertinent when using
> GB,
> as they define the various intrinsic radii used by GB. The new version of
> AMBER - AMBER11 - will have new intrinsic radii, parametrized using massive
> training sets. To answer your question, the quality of PB comes from
> calculating the intrinsic radii, so mbondi and mbondi ought not affect the
> results too much. However, it is common practice to always specify mbondi2,
> even if you're using TIP3P. Unless you want mbondi instead of mbondi2 - say
> previous work on your proposed work has shown better results, however
> unlikely - then go with it. But otherwise, specify mbondi2, even when using
> PB.
>
>
> Hope this helps,
> kevin
>
> On Sun, Mar 21, 2010 at 3:55 PM, s. Bill <s_bill36.yahoo.co.uk> wrote:
>
> > Dear AMBERUsing mbondi or mbondi2 affects MD simulation? In other words,
> > the resulted MD trajectories will be different in case I used mbondi
> instead
> > of mbondi2.Or it just makes sense during MM-PBSA calculation?Thanks in
> > advanceS. bill
> >
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -- - -
> HK
>
> -------------------------------------------------------
> Kevin Eduard Hauser
>
> The Department of Chemistry
>
> Stony Brook University
> Stony Brook, New York 11794
>
> (631) 913.3194
> (561) 635.1848
>
> 84hauser.gmail.com
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Received on Sun Mar 21 2010 - 14:30:02 PDT
