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
> > **
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 26 2011 - 06:00:05 PDT
