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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Received on Fri Sep 01 2017 - 06:30:05 PDT
