Hi all,
We have carried microsecond simulations for a protein (800 aa) - RNA (17
bp) systems. Various modified RNA molecules have been used to find the
binding specificity/affinity with the same protein. The free energy of
binding was calculated using MM-PBSA method. The entropic contribution was
calculated using NMODE method. The free energy values (dG) are in the
range of -250 kcal/mol. However, among the various systems used, the
difference in the free energy values(ddG) are in the range of 10 to 30
kcal/mol. These numbers are more or less to similar to the standard
deviation of the free energy obtained MM-PBSA calculations. Are these
error values obtained from the calculations quantitatively correct? Is it
safe to report such free energy changes in publications. If not, is there
any other better way to calculate the absolute free energy other than
approximation methods using AMBER package?
Harikrishna
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Received on Tue Sep 13 2016 - 23:00:02 PDT
