Dear Dr. Simmerling,
Thank you very much for your advice.
Regards,
Chinh
On Sat, Aug 27, 2011 at 9:26 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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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Received on Sat Aug 27 2011 - 08:00:02 PDT
