Dear Sir/Madam,
I am doing a calculation for a DNA-protein complexes, I found the binding energy (GBTOT= ELE + VDW + GBSUR + GB) is around -120 in the GBSA output file.
Could you mind to let me know if it is in kJ/mol unit?
I found it is about 2-3 fold higher than those of the protein-protein interactions (GBTOT = -60). Given I did not do the DS calculations, do you think it is a reasonable number?
Given I did not do the DS analysis, can I directly compare these values with a protein-protein complex to say that the binding between protein-protein complexes is weaker than that of the DNA-protein complex? I guess the answer is NO, because I cannot cancel out the DS for structurallly dissimilar molecules.
Best regards,
Catherine
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Received on Tue Aug 09 2011 - 01:00:02 PDT
