Thank you for your help sincerely. Both you and Prof. Case’s suggestions
are really helpful.
Jacky
Carlos Simmerling <carlos.simmerling.gmail.com>于2017年9月1日 周五下午9:29写道：
> just to add to the good advice Dave gave you, I'm not sure if I interpret
> the results of that article the same way you stated. There are a few things
> to keep in mind with regard to that specific study:
> 1) the authors state many times that the results are not well converged and
> replicate runs often gave different results.
> 2) capped vs uncapped results were not usually different from each other.
> 3) it is unclear what "accurate" means in this case, because there are no
> quantitative experimental structure data corresponding to the peptide that
> was simulated. The article is very useful in terms of seeing how the
> different force fields have different propensities, but lack of
> quantitative experimental data for validation tells me to be cautious in
> using the details to draw more general conclusions such as that capping
> leads to more accurate or less accurate simulations. In other words, in
> this case it isn't clear what the "real" answer should be.
>
> I think the best advice we can give you is what Dave also suggested: try as
> best as possible to simulate what is in the experiment (or biology) that
> you are trying to understand. If the system is capped, or uncapped, or at
> an unusual pH or temperature, and so on, try to deviate as little as
> possible from those conditions until you gain experience.
>
> On Fri, Sep 1, 2017 at 8:42 AM, David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Fri, Sep 01, 2017, jacky zhao wrote:
> > >
> > > Therefore, I am wondering the role of ACE and NME capping protein in
> the
> > > protein simulation.
> >
> > At the risk of telling you what you already know:
> >
> > Chemists who synthesize peptides often add capping groups, for various
> > reasons.
> > The ACE and NME/NHE caps are provided in the Amber libraries so that
> > simulations can be made on such artificial systems.
> >
> > Cells (at least in the vast majority of cases) don't cap anything; if
> there
> > is something other than an ordinary (charged) amino acid at the N- or
> > C-terminus, it would be considered a post-translational modification (and
> > would
> > probably have a different chemistry than ACE or NME.)
> >
> > Generally, to simulate an "ordinary" protein, one would not use capping
> > groups.
> > (There are, of course, exceptions to every rule, and others on the list
> > might
> > want to chime in.) In standard usage, ACE and NME capping groups would
> > only be called for when dealing with synthetic peptides.
> >
> > ....dac
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
Lei Zhao, Ph.D.
International Joint Cancer Institute of the Second Military Medical
University
National Engineering Research Center for Antibody Medicine
New Library Building 11th floor,800 Xiang Yin Road
Shanghai 200433
P.R.China
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Received on Fri Sep 01 2017 - 09:00:04 PDT
