In water? peptide secondary structures are difficult to get quantitatively
right using most current GB models- these is fairly well documented in the
literature. Whether these will work for you depends on whether you're
looking for qualitative or quantitative answers. igb=5 is perhaps the best
choice in Amber among the GB models that are published, though it does
overstabilize helices; I think igb=8 is significantly better but we're
still preparing a manuscript that describes all of the details so at the
moment it's probably best used by experts.
My opinion is that the manual, archives and email list are great places to
go to find out about how to best use Amber, and what the various options
do. For actually deciding what types of simulations you *should* do,
however, I often tell people that the peer-reviewed literature is the place
to go. If you don't have enough experience on your own to know what type of
simulation will suit your needs, the best option by far is to read articles
that were trying to answer questions similar to your own, and see what they
did to successfully answer them. Then, you can ask here or other places to
find out how you might implement this kind of simulation.
On Aug 22, 2012 9:52 PM, "Elaine Cheung" <playbutplay.126.com> wrote:
>
>
>
>
>
> I am trying to learn about the secondary structure of the peptide by using
> SMD method.
> At 2012-08-22 17:28:26,"Carlos Simmerling" <carlos.simmerling.gmail.com>
> wrote:
> >What are you trying to learn?
> >On Aug 22, 2012 1:57 PM, "Elaine Cheung" <playbutplay.126.com> wrote:
> >
> >> Hi,
> >> I am trying to build a system of gp41 peptide by using force field
> ff99SB
> >> and ff12SB under surface area. I use the command "set default PBradii
> >> mbondi2" to prepare the prmtop file. But I don't know which value I
> should
> >> choose for igb in the mdin file, igb=2 or igb=5? Which one is better for
> >> the force field ff99SB and ff12SB?
> >>
> >>
> >> Best,
> >> Elaine
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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Received on Sat Aug 25 2012 - 05:00:03 PDT
