Dear Amber users,
This is more of a general doubt and I would like to know if it can be
addressed by MMPBSA. I have a DNA system in different solvents for a
comparative study. The DNA conformation varies slightly in the different
systems but maintains overall the B-DNA conformation. The DNA interacts
with the solvent molecules. I would like to know which of the solvents
solvate DNA best, i.e, has the highest solvation energy (is that correct).
So can I use the Gsolv term in MMPBSA (the dielectrics of the different
solvents are different and I have included them in the calculation) to make
this comparison? I have come across several papers which have compared
different conformations of DNA in different solvents, but here there is
only little change in conformation.
Thanks in advance for any help
--
Debostuti
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Received on Sun Feb 10 2013 - 22:00:02 PST
