you should try to become more familiar with the protein folding literature
before undertaking such a project. Perhaps read recent papers by the DE Shaw
team, and other labs. Identification of saddle points in folding of large
proteins like yours is far from routine.
On Fri, Aug 26, 2011 at 8:51 AM, Chinh Su Tran To
<chinh.sutranto.gmail.com>wrote:
> Dear Dr. Simmerling,
>
> I want to detect intermediate states of the target protein, or exactly that
> i want to extract the "saddle point" states (which show the energy shift).
> When I first started the project, the experimental structure was not
> available, so I started with homology modeling to get the initial structure
> of the protein. After running short minimization and short-time refinement
> for the structure, I got the structure which reached the equilibrium.
> Thus, I ran again with longer time for the MD (20ns), and I want to
> *unfold*it again (im not quite sure HOW, but im still doing trials).
> Any suggestions
> will be definitely useful for me, and I am greatly thankful for that.
>
> >From the second point, did you suggest me NOT using the homology modeling,
> but start to fold the protein from scratch (from the sequence)? I will try
> from this.
> Thank you very much for your advice.
>
> Chinsu
>
> On Fri, Aug 26, 2011 at 7:29 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > the rmsd values after that point all seem low, so it probably is stuck in
> > some minimum. is that the global minimum? there is no way to know from
> this
> > data. you might want to try running several simulations to see if this is
> > reproducible, and perhaps from different initial structures as well.
> >
> >
> > keep in mind you might be seeing some local rearrangement of your
> homology
> > model- but what you are modeling in a few ns almost certainly should not
> be
> > called "protein folding". you will need to be much more clear about what
> > you
> > are doing, what experimental data you have, and what you want to learn.
> > this
> > doesn't sound like a protein folding project.
> >
> > On Fri, Aug 26, 2011 at 6:16 AM, Chinh Su Tran To
> > <chinh.sutranto.gmail.com>wrote:
> >
> > > Hi AMBER users,
> > >
> > > I have some doubts, could you please help me to explain them?
> > >
> > > I run a 20ns MD simulation for my protein (158 aa) to detect the
> protein
> > > folding process. The protein was modeled using a template (homology
> > > modeling) before running MD.
> > > Firstly, I ran a short minimization for the protein, then a heating
> > process
> > > was conducted in 20ps, and followed by a 10-stage MD run (2ns for
> each).
> > >
> > > I got the result, and extracted the lowest energy structure at 6.934 ns
> > > (frame 457 of the md4.mdcrd). *Does this mean that my protein obtained
> > the
> > > folded state at this point of time or it just was trapped in some local
> > > minima? *because at time point 6.934ns is it very "early" compared to
> the
> > > whole process of 20ns?
> > >
> > > Then I plotted the backbone_RMS of the 10 stage results (compared to
> the
> > > lowest energy structure). The plot was attached here too. It turned out
> > > that
> > > there were some other time points showing stable RMS fluctuations too.
> As
> > > referred to the tutorial, *does the result show that the protein kept
> > > folding and unfolding during the time?*
> > > *
> > > *
> > > And one more question is how come the plot only showed up with 10,000
> ps
> > in
> > > the x-axis.
> > >
> > > *trajin ../ndm_md1.mdcrd
> > > trajin ../ndm_md2.mdcrd
> > > trajin ../ndm_md3.mdcrd
> > > trajin ../ndm_md4.mdcrd
> > > trajin ../ndm_md5.mdcrd
> > > trajin ../ndm_md6.mdcrd
> > > trajin ../ndm_md7.mdcrd
> > > trajin ../ndm_md8.mdcrd
> > > trajin ../ndm_md9.mdcrd
> > > trajin ../ndm_md10.mdcrd
> > > reference E_lowest_457.pdb
> > > rms reference out rms_to_457 .N,CA,C time 1.0
> > >
> > > *Thank you very much for any help.
> > >
> > > Regards,
> > > Chinsu
> > > **
> > >
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> > >
> > >
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> >
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Received on Sat Aug 27 2011 - 06:30:02 PDT
