AMBER Archive (2006)Subject: AMBER: about the std of computational alanine scanning
From: tongli (tong.li_at_rega.kuleuven.be)
Date: Fri Dec 01 2006  05:50:11 CST
Dear colleagues
I have met a problem when I used Computational Alanine Scanning to
calculate the binding free energy. Normally we can calculate the
ÄGwildtype and ÄGmutant respectively and only got the final values of
ÄG with their own std and we calculate the ÄÄG by this equation
ÄÄG=ÄGwildtypeÄGmutant. But it seems difficult to get the std of ÄÄG
automatically because we just use two values, one from the ÄGwildtype
and one from the ÄGmutant. It will be very complex to extract every term
from the ÄGwildtype and ÄGmutant separately and calculate the std
manually. Can I modify the mm_pbsa.pl to make this calculation
automatically or some other suggestions?
Thanks in advance!
Tong Li
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