> 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?
Yes, I retain all of the atoms of the full protein, but break one peptide bond to form a ligand and receptor.
> 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.
Sorry to be vague. For calculation of the MM-GB or PBSA energies, I get ridiculous numbers. But they only come from one of the two subunits (the one I set as the ligand).
For calculation of decomposed energies (which I do with GB, as I am using Amber 10), the problem I run into is that random residues return values of **********. So they fail because they are missing numbers for particular residues. For example, I get
TDC 573 22914.777 ********* 12.994 -160.534 90.979
I have run into a similar problem before, but it had always been giving errors for the same residue in each snapshot.
TDC 573 22611.434 46476.477 30.092 -160.260 99.821
As you can see, this isn't the case here, as that is data from the same residue, but a different snapshot. I don't know why this is happening, and structurally I see nothing wrong with the residues.
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Received on Thu Mar 21 2013 - 12:30:02 PDT
