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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Received on Fri Aug 26 2011 - 05:00:03 PDT
