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.
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.
In addition, the residues that are causing problems are not consistent from snapshot to snapshot. In the past, I've had problems similar to this because of errors in defining my ligand and receptor, but that always caused an error on the same residue.
Has anyone ever seen any errors like this? I'd appreciate any ideas/suggestions anyone can give me.
Thanks!
Amy Migliori, UCSD physics/biochemistry
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Received on Tue Mar 19 2013 - 17:30:02 PDT
