Dear all,
I am running some MMPBSA post-processing calculations on a ternary system composed by PROTEIN, DNA and a LIGAND intercalating the dna.
I am considering the protein/dna complex as the RECEPTOR, whereas the intercalating ligand is (effectively) the LIGAND.
A total of 60 frames is processed on 12 processors (5 frames per processor).
I am using the non-linearized PB equation for deriving the binding free energies in the thermodynamic cycle.
In my system, there are six cocrystallized Mg2+ ions that are crucial for anchoring the DNA to the protein and for attaining the catalytic mechanism. Therefore, these Mg2+ can not be deleted.
I wonder if there is any particular procedure for the treatment of the Mg2+ ions in MMPBSA calculations, using the non-linearized PB equation.
Do you have any suggestion??
thank you very much
Giulia
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Received on Thu Mar 21 2013 - 08:30:02 PDT
