Hi,
I was having a look at the GBSA tutorials and had a query that someone
might help to resolve.
Looking at the following page:
http://ringo.ams.sunysb.edu/index.php/2011_AMBER_Tutorial_with_Biotin_and_Streptavidin#MMGBSA
It says that:
ÄGnonpolar = SASA*0.00542 + 0.92
I understand that the 0.00542 + 0.92 term is a correction term for MM-PBSA.
Where:
SURFTEN 0.00542
SURFOFF 0.92
However, when running GBSA using the sander module (igb=1), I saw someone
in the archives mention that the correct value for surften was 0.0072. So
My question is whether surften becomes 0.0072 in the infile and becomes
ÄGnonpolar = SASA*0.0072 or if the previous values are correct.
Thanks in advance,
ET
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Received on Tue Mar 20 2012 - 11:00:02 PDT
