Dear AMBER users,
I have done mmpbsa binding free energy calculations on a 10-mer DNA
structures using MMPBSA.py script. The MMGBSA binding free energy
value changes from -43 kcal mol-1 to -60 kcal mol when included the
saltcon parameter (saltcon=0.1). But the MMPBSA value doesnt show any
significant change. only about ~0.5-0.7 kcal mol-1. what is the
actural role of the saltcon as we are neutrilzaing the system before
we do simulation..?
Also one more doubt for me..
The EEL and EGB/EPB values are almost very close, but opposite in
sign..I got values like 1239 and -1208 kcal mol-1.
Any idea or explantions ..
Thanks
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Received on Tue Sep 13 2011 - 17:00:02 PDT
