I don't think there is a cut-and-dry answer to this question. If the
flexible loop plays a strong role in binding, then it is probably unlikely
that MM/GBSA will give you reliable results. However, MM/GBSA is really
only good for relative free energies anyway, so it may be fine, as long as
the mobile loop is doing the same thing in each simulation (that seems
difficult to me to prove, especially if it's playing a strong role in
binding).
One thing you can do to check is to run separate MM/PB(GB)SA calculations on
several different chunks of your trajectory and compare those. Since you
said that the rest of the domains had stabilized, any large differences
between the results for the different chunks may be due to the mobile loop.
Others may chime in with more advice/suggestions.
Good luck!
Jason
On Sun, Jun 13, 2010 at 12:00 PM, Catein Catherine
<askamber23.hotmail.com>wrote:
>
> Dear Sir/Madam,
>
>
>
> A protein with two domains. I did a MD simulation for the system, but I
> found no matter how long I did the simulation, the RMSD did not become
> stable and go as high as 4 A. However, when I did the RMSD analysis without
> the flexible domain, it become stable in 200ps and the rest of the domains
> is stable for a the whole long simulation period with RMSD of 2A.
>
>
>
> Can you share your experience with me if it is necessary to wait till all
> domains become stable, or can we report the movement, PCA analysis for the
> system to illustrate the transition or the movement of the flexible domain?
>
>
>
> Can I did the MM/GBSA analysis even the whole system did not equilibrated
> yet?
>
>
>
> Best regards,
>
>
>
> Cat
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Jun 13 2010 - 10:00:05 PDT
