On Tue, Mar 19, 2013 at 8:27 PM, Amy Davenport <adavenpo.ucsd.edu> wrote:
> Hi all,
> I'm hoping someone can help me figure out how to calculate the mmgb dc
> energies for the interface between two subunits in a large complex. I have
> done this type of calculation before, for a single protein that has been
> cut to form the ligand and receptor with little problem.
>
When you say 'cut', you mean what you call the 'receptor' and 'ligand' are
covalently bound?
> This time, the overall complex is made up of two identical proteins (in
> sequence, not position). I have designated one of them the ligand and one
> the receptor for the purposes of this calculation. Both DC and non
> decomposed free energy calculations work well for one of the two proteins,
> and for some reason fail for the second. I have tried switching the ligand
> and receptor definitions, and it still fails for the second, regardless of
> which it is.
>
You need to be more specific. We have no way of knowing what "failed"
means -- different 'failures' are indicative of different problems. Did
the calculation die with an error message? (If so, we need to know exactly
how you got the error and what that error message is). Do you just get
ridiculous numbers? Do you get a warning? Etc.
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Mar 20 2013 - 06:30:04 PDT
